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dream_challenge.sh
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#1 , 3029328166, order: 3, svr: scg, old #: 38
NTH=6; SUFFIX="CHIPseq.ATF2.GM12878.EXPID_ENCSR000BQK"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.ATF2.GM12878.EXPID_ENCSR000BQK.BSID_ENCBS110ENC.BSREP2.TECHREP1.FILEIDENCFF000NSG.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.ATF2.GM12878.EXPID_ENCSR000BQK.BSID_ENCBS110ENC.BSREP1.TECHREP1.FILEIDENCFF000NSE.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.GM12878.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#2 , 3001020425, order: 3, svr: scg, old #: 42
NTH=12; SUFFIX="CHIPseq.ATF2.H1-hESC.EXPID_ENCSR000BQU"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.ATF2.H1-hESC.EXPID_ENCSR000BQU.BSID_ENCBS111ENC.BSREP2.TECHREP1.FILEIDENCFF000OMY.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.ATF2.H1-hESC.EXPID_ENCSR000BQU.BSID_ENCBS111ENC.BSREP1.TECHREP1.FILEIDENCFF000OMR.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.H1-hESC.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.H1-hESC/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.H1-hESC/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#3 , 3788075584, order: 4, svr: scg, old #: 12
NTH=7; SUFFIX="CHIPseq.CREB1.K562.EXPID_ENCSR000BSO"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CREB1.K562.EXPID_ENCSR000BSO.BSID_ENCBS109ENC.BSREP2.TECHREP1.FILEIDENCFF000PYC.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CREB1.K562.EXPID_ENCSR000BSO.BSID_ENCBS109ENC.BSREP1.TECHREP1.FILEIDENCFF000PXY.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.K562.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.K562/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.K562/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#4 , 3515603354, order: 4, svr: scg, old #: 14
NTH=7; SUFFIX="CHIPseq.CREB1.HepG2.EXPID_ENCSR000BVL"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CREB1.HepG2.EXPID_ENCSR000BVL.BSID_ENCBS114ENC.BSREP2.TECHREP1.FILEIDENCFF000PGZ.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CREB1.HepG2.EXPID_ENCSR000BVL.BSID_ENCBS114ENC.BSREP1.TECHREP1.FILEIDENCFF000PGX.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HepG2.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#5 , 3356225874, order: 4, svr: scg, old #: 23
NTH=6; SUFFIX="CHIPseq.CREB1.H1-hESC.EXPID_ENCSR000BSN"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CREB1.H1-hESC.EXPID_ENCSR000BSN.BSID_ENCBS111ENC.BSREP2.TECHREP1.FILEIDENCFF000ONP.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CREB1.H1-hESC.EXPID_ENCSR000BSN.BSID_ENCBS111ENC.BSREP1.TECHREP1.FILEIDENCFF000ONS.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.H1-hESC.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.H1-hESC/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.H1-hESC/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#6 , 2763165890, order: 4, svr: scg, old #: 57
NTH=5; SUFFIX="CHIPseq.CREB1.GM12878.EXPID_ENCSR000BUF"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CREB1.GM12878.EXPID_ENCSR000BUF.BSID_ENCBS110ENC.BSREP2.TECHREP1.FILEIDENCFF000NUL.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CREB1.GM12878.EXPID_ENCSR000BUF.BSID_ENCBS110ENC.BSREP1.TECHREP1.FILEIDENCFF000NUK.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.GM12878.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#7 , 3031926935, order: 6, svr: scg, old #: 37
NTH=6; SUFFIX="CHIPseq.EGR1.MCF-7.EXPID_ENCSR000BUX"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.EGR1.MCF-7.EXPID_ENCSR000BUX.BSID_ENCBS056AAA.BSREP1.TECHREP1.FILEIDENCFF000QMF.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.EGR1.MCF-7.EXPID_ENCSR000BUX.BSID_ENCBS056AAA.BSREP2.TECHREP1.FILEIDENCFF000QMC.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.MCF-7.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#8 , 2378948392, order: 6, svr: scg, old #: 91
NTH=4; SUFFIX="CHIPseq.EGR1.HCT116.EXPID_ENCSR000BRZ"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.EGR1.HCT116.EXPID_ENCSR000BRZ.BSID_ENCBS389ENC.BSREP2.TECHREP1.FILEIDENCFF000OZL.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.EGR1.HCT116.EXPID_ENCSR000BRZ.BSID_ENCBS389ENC.BSREP1.TECHREP1.FILEIDENCFF000OZI.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HCT116.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HCT116/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HCT116/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#9 , 2175239415, order: 6, svr: scg, old #: 115
NTH=4; SUFFIX="CHIPseq.EGR1.K562.EXPID_ENCSR000BNE"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.EGR1.K562.EXPID_ENCSR000BNE.BSID_ENCBS109ENC.BSREP2.TECHREP1.FILEIDENCFF000PZP.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.EGR1.K562.EXPID_ENCSR000BNE.BSID_ENCBS109ENC.BSREP1.TECHREP1.FILEIDENCFF000PZK.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.K562.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.K562/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.K562/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#10 , 1945016423, order: 6, svr: scg, old #: 154
NTH=3; SUFFIX="CHIPseq.EGR1.GM12878.EXPID_ENCSR000BMQ"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.EGR1.GM12878.EXPID_ENCSR000BMQ.BSID_ENCBS110ENC.BSREP2.TECHREP1.FILEIDENCFF000NVF.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.EGR1.GM12878.EXPID_ENCSR000BMQ.BSID_ENCBS110ENC.BSREP1.TECHREP1.FILEIDENCFF000NVC.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.GM12878.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#11 , 4082233956, order: 7, svr: scg, old #: 8
NTH=8; SUFFIX="CHIPseq.TCF12.SK-N-SH.EXPID_ENCSR000BSL"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TCF12.SK-N-SH.EXPID_ENCSR000BSL.BSID_ENCBS428ENC.BSREP1.TECHREP1.FILEIDENCFF000REF.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TCF12.SK-N-SH.EXPID_ENCSR000BSL.BSID_ENCBS428ENC.BSREP2.TECHREP1.FILEIDENCFF000REA.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.SK-N-SH.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.SK-N-SH/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.SK-N-SH/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#12 , 3050211475, order: 7, svr: scg, old #: 35
NTH=6; SUFFIX="CHIPseq.TCF12.MCF-7.EXPID_ENCSR000BUN"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TCF12.MCF-7.EXPID_ENCSR000BUN.BSID_ENCBS056AAA.BSREP1.TECHREP1.FILEIDENCFF000QRV.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TCF12.MCF-7.EXPID_ENCSR000BUN.BSID_ENCBS056AAA.BSREP2.TECHREP1.FILEIDENCFF000QRU.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.MCF-7.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#13 , 2336134430, order: 7, svr: scg, old #: 98
NTH=4; SUFFIX="CHIPseq.TCF12.HepG2.EXPID_ENCSR000BJG"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TCF12.HepG2.EXPID_ENCSR000BJG.BSID_ENCBS114ENC.BSREP2.TECHREP1.FILEIDENCFF000PRL.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TCF12.HepG2.EXPID_ENCSR000BJG.BSID_ENCBS114ENC.BSREP1.TECHREP1.FILEIDENCFF000PRJ.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HepG2.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#14 , 1860613653, order: 7, svr: scg, old #: 171
NTH=3; SUFFIX="CHIPseq.TCF12.GM12878.EXPID_ENCSR000BGZ"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TCF12.GM12878.EXPID_ENCSR000BGZ.BSID_ENCBS110ENC.BSREP1.TECHREP1.FILEIDENCFF000OGQ.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TCF12.GM12878.EXPID_ENCSR000BGZ.BSID_ENCBS110ENC.BSREP2.TECHREP1.FILEIDENCFF000OGN.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.GM12878.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#15 , 2705417779, order: 8, svr: scg, old #: 60
NTH=5; SUFFIX="CHIPseq.TCF7L2.HeLa-S3.EXPID_ENCSR000EVE"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TCF7L2.HeLa-S3.EXPID_ENCSR000EVE.BSID_ENCBS500SDW.BSREP2.TECHREP1.FILEIDENCFF000XMN.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TCF7L2.HeLa-S3.EXPID_ENCSR000EVE.BSID_ENCBS500SDW.BSREP1.TECHREP1.FILEIDENCFF000XML.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HeLa-S3.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HeLa-S3/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HeLa-S3/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#16 , 2096290597, order: 8, svr: scg, old #: 129
NTH=4; SUFFIX="CHIPseq.TCF7L2.HEK293.EXPID_ENCSR000EUY"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TCF7L2.HEK293.EXPID_ENCSR000EUY.BSID_ENCBS479AAA.BSREP1.TECHREP1.FILEIDENCFF000WYK.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TCF7L2.HEK293.EXPID_ENCSR000EUY.BSID_ENCBS479AAA.BSREP2.TECHREP1.FILEIDENCFF000WYN.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HEK293.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HEK293/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HEK293/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out
sleep 5
#17 , 1979604643, order: 8, svr: scg, old #: 146
NTH=3; SUFFIX="CHIPseq.TCF7L2.MCF-7.EXPID_ENCSR000EWT"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TCF7L2.MCF-7.EXPID_ENCSR000EWT.BSID_ENCBS105ENC.BSREP2.TECHREP1.FILEIDENCFF000ZLM.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TCF7L2.MCF-7.EXPID_ENCSR000EWT.BSID_ENCBS105ENC.BSREP1.TECHREP1.FILEIDENCFF000ZLK.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.MCF-7.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#18 , 1948301642, order: 8, svr: scg, old #: 153
NTH=3; SUFFIX="CHIPseq.TCF7L2.HepG2.EXPID_ENCSR000EVQ"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TCF7L2.HepG2.EXPID_ENCSR000EVQ.BSID_ENCBS950MSQ.BSREP1.TECHREP1.FILEIDENCFF000XYV.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TCF7L2.HepG2.EXPID_ENCSR000EVQ.BSID_ENCBS950MSQ.BSREP2.TECHREP1.FILEIDENCFF000XYX.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HepG2.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#19 , 1115417311, order: 8, svr: scg, old #: 246
NTH=20; SUFFIX="CHIPseq.TCF7L2.HeLa-S3.EXPID_ENCSR000EVF"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TCF7L2.HeLa-S3.EXPID_ENCSR000EVF.BSID_ENCBS500SDW.BSREP1.TECHREP1.FILEIDENCFF000XMD.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TCF7L2.HeLa-S3.EXPID_ENCSR000EVF.BSID_ENCBS500SDW.BSREP2.TECHREP1.FILEIDENCFF000XMF.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HeLa-S3.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HeLa-S3/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HeLa-S3/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#20 , 2860865649, order: 10, svr: scg, old #: 51
NTH=5; SUFFIX="CHIPseq.FOXA2.HepG2.EXPID_ENCSR000BNI"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.FOXA2.HepG2.EXPID_ENCSR000BNI.BSID_ENCBS114ENC.BSREP2.TECHREP1.FILEIDENCFF000PIX.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.FOXA2.HepG2.EXPID_ENCSR000BNI.BSID_ENCBS114ENC.BSREP1.TECHREP1.FILEIDENCFF000PIT.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HepG2.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#21 , 1063787657, order: 11, svr: scg, old #: 249
NTH=3; SUFFIX="CHIPseq.HNF4A.HepG2.EXPID_ENCSR000BLF"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.HNF4A.HepG2.EXPID_ENCSR000BLF.BSID_ENCBS114ENC.BSREP2.TECHREP1.FILEIDENCFF000PJX.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.HNF4A.HepG2.EXPID_ENCSR000BLF.BSID_ENCBS114ENC.BSREP1.TECHREP1.FILEIDENCFF000PJT.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HepG2.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 20000000
##SUBSAMPLED CTL (20M)!
sleep 5
#22 , 980290758, order: 12, svr: scg, old #: 253
NTH=20; SUFFIX="CHIPseq.FOXA1.HepG2.EXPID_ENCSR000BMO"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.FOXA1.HepG2.EXPID_ENCSR000BMO.BSID_ENCBS114ENC.BSREP1.TECHREP1.FILEIDENCFF000PIB.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.FOXA1.HepG2.EXPID_ENCSR000BMO.BSID_ENCBS114ENC.BSREP2.TECHREP1.FILEIDENCFF000PHY.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HepG2.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#23 , 4024463809, order: 13, svr: scg, old #: 10
NTH=8; SUFFIX="CHIPseq.TAF1.MCF-7.EXPID_ENCSR000AHF"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TAF1.MCF-7.EXPID_ENCSR000AHF.BSID_ENCBS000AAA.BSREP1.TECHREP1.FILEIDENCFF000QRS.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TAF1.MCF-7.EXPID_ENCSR000AHF.BSID_ENCBS001AAA.BSREP2.TECHREP1.FILEIDENCFF000QRL.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.MCF-7.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#24 , 2960372979, order: 13, svr: scg, old #: 46
NTH=5; SUFFIX="CHIPseq.TAF1.SK-N-SH.EXPID_ENCSR000BQF"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TAF1.SK-N-SH.EXPID_ENCSR000BQF.BSID_ENCBS428ENC.BSREP1.TECHREP1.FILEIDENCFF000RDS.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TAF1.SK-N-SH.EXPID_ENCSR000BQF.BSID_ENCBS428ENC.BSREP2.TECHREP1.FILEIDENCFF000RDR.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.SK-N-SH.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.SK-N-SH/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.SK-N-SH/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#25 , 2445217858, order: 13, svr: scg, old #: 81
NTH=4; SUFFIX="CHIPseq.TAF1.GM12891.EXPID_ENCSR000BIM"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TAF1.GM12891.EXPID_ENCSR000BIM.BSID_ENCBS388ENC.BSREP1.TECHREP1.FILEIDENCFF000OKG.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TAF1.GM12891.EXPID_ENCSR000BIM.BSID_ENCBS388ENC.BSREP2.TECHREP1.FILEIDENCFF000OKD.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.GM12891.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12891/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12891/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out
sleep 5
#26 , 2432950687, order: 13, svr: scg, old #: 83
NTH=4; SUFFIX="CHIPseq.TAF1.HeLa-S3.EXPID_ENCSR000BHT"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TAF1.HeLa-S3.EXPID_ENCSR000BHT.BSID_ENCBS113ENC.BSREP1.TECHREP1.FILEIDENCFF000PFL.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TAF1.HeLa-S3.EXPID_ENCSR000BHT.BSID_ENCBS113ENC.BSREP2.TECHREP1.FILEIDENCFF000PFJ.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HeLa-S3.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HeLa-S3/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HeLa-S3/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#27 , 2420566328, order: 13, svr: scg, old #: 85
NTH=4; SUFFIX="CHIPseq.TAF1.HepG2.EXPID_ENCSR000BJN"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TAF1.HepG2.EXPID_ENCSR000BJN.BSID_ENCBS114ENC.BSREP1.TECHREP1.FILEIDENCFF000PRD.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TAF1.HepG2.EXPID_ENCSR000BJN.BSID_ENCBS114ENC.BSREP2.TECHREP1.FILEIDENCFF000PRB.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HepG2.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#28 , 2263206380, order: 13, svr: scg, old #: 104
NTH=4; SUFFIX="CHIPseq.TAF1.GM12892.EXPID_ENCSR000BIB"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TAF1.GM12892.EXPID_ENCSR000BIB.BSID_ENCBS055ENC.BSREP1.TECHREP1.FILEIDENCFF000OMD.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TAF1.GM12892.EXPID_ENCSR000BIB.BSID_ENCBS055ENC.BSREP2.TECHREP1.FILEIDENCFF000OLZ.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.GM12892.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12892/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12892/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#29 , 1775963148, order: 13, svr: scg, old #: 185
NTH=3; SUFFIX="CHIPseq.TAF1.GM12878.EXPID_ENCSR000BGS"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.TAF1.GM12878.EXPID_ENCSR000BGS.BSID_ENCBS110ENC.BSREP2.TECHREP1.FILEIDENCFF000OGH.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.TAF1.GM12878.EXPID_ENCSR000BGS.BSID_ENCBS110ENC.BSREP1.TECHREP1.FILEIDENCFF000OGC.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.GM12878.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#30 , 3475812444, order: 14, svr: scg, old #: 16
NTH=6; SUFFIX="CHIPseq.GABPA.SK-N-SH.EXPID_ENCSR000BTG"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.GABPA.SK-N-SH.EXPID_ENCSR000BTG.BSID_ENCBS428ENC.BSREP2.TECHREP1.FILEIDENCFF000QYW.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.GABPA.SK-N-SH.EXPID_ENCSR000BTG.BSID_ENCBS428ENC.BSREP1.TECHREP1.FILEIDENCFF000QYP.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.SK-N-SH.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.SK-N-SH/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.SK-N-SH/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#31 , 3277944844, order: 14, svr: scg, old #: 27
NTH=6; SUFFIX="CHIPseq.GABPA.MCF-7.EXPID_ENCSR000BUK"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.GABPA.MCF-7.EXPID_ENCSR000BUK.BSID_ENCBS056AAA.BSREP1.TECHREP1.FILEIDENCFF000QNK.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.GABPA.MCF-7.EXPID_ENCSR000BUK.BSID_ENCBS056AAA.BSREP2.TECHREP1.FILEIDENCFF000QNJ.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.MCF-7.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#32 , 3081693799, order: 14, svr: scg, old #: 33
NTH=6; SUFFIX="CHIPseq.GABPA.HepG2.EXPID_ENCSR000BJK"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.GABPA.HepG2.EXPID_ENCSR000BJK.BSID_ENCBS114ENC.BSREP1.TECHREP1.FILEIDENCFF000PJF.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.GABPA.HepG2.EXPID_ENCSR000BJK.BSID_ENCBS114ENC.BSREP2.TECHREP1.FILEIDENCFF000PJC.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HepG2.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#33 , 2651282313, order: 14, svr: scg, old #: 65
NTH=5; SUFFIX="CHIPseq.GABPA.HeLa-S3.EXPID_ENCSR000BHS"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.GABPA.HeLa-S3.EXPID_ENCSR000BHS.BSID_ENCBS113ENC.BSREP2.TECHREP1.FILEIDENCFF000PEK.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.GABPA.HeLa-S3.EXPID_ENCSR000BHS.BSID_ENCBS113ENC.BSREP1.TECHREP1.FILEIDENCFF000PEH.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HeLa-S3.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HeLa-S3/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HeLa-S3/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#34 , 2523479647, order: 14, svr: scg, old #: 74
NTH=5; SUFFIX="CHIPseq.GABPA.HL-60.EXPID_ENCSR000BTK"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.GABPA.HL-60.EXPID_ENCSR000BTK.BSID_ENCBS070ENC.BSREP1.TECHREP1.FILEIDENCFF000PTV.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.GABPA.HL-60.EXPID_ENCSR000BTK.BSID_ENCBS070ENC.BSREP2.TECHREP1.FILEIDENCFF000PTU.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HL-60.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HL-60/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HL-60/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#35 , 2442710718, order: 14, svr: scg, old #: 82
NTH=4; SUFFIX="CHIPseq.GABPA.GM12878.EXPID_ENCSR000BGC"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.GABPA.GM12878.EXPID_ENCSR000BGC.BSID_ENCBS110ENC.BSREP1.TECHREP1.FILEIDENCFF000NWM.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.GABPA.GM12878.EXPID_ENCSR000BGC.BSID_ENCBS110ENC.BSREP2.TECHREP1.FILEIDENCFF000NWN.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.GM12878.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#36 , 3011601864, order: 15, svr: scg, old #: 40
NTH=6; SUFFIX="CHIPseq.CEBPB.A549.EXPID_ENCSR000BUB"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CEBPB.A549.EXPID_ENCSR000BUB.BSID_ENCBS164AAA.BSREP1.TECHREP1.FILEIDENCFF000MXK.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CEBPB.A549.EXPID_ENCSR000BUB.BSID_ENCBS164AAA.BSREP2.TECHREP1.FILEIDENCFF000MXH.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.A549.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.A549/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.A549/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#37 , 2863350953, order: 15, svr: scg, old #: 50
NTH=5; SUFFIX="CHIPseq.CEBPB.HCT116.EXPID_ENCSR000BSD"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CEBPB.HCT116.EXPID_ENCSR000BSD.BSID_ENCBS389ENC.BSREP2.TECHREP1.FILEIDENCFF000OYU.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CEBPB.HCT116.EXPID_ENCSR000BSD.BSID_ENCBS389ENC.BSREP1.TECHREP1.FILEIDENCFF000OYS.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HCT116.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HCT116/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HCT116/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#38 , 2604175371, order: 15, svr: scg, old #: 67
NTH=5; SUFFIX="CHIPseq.CEBPB.MCF-7.EXPID_ENCSR000BSR"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CEBPB.MCF-7.EXPID_ENCSR000BSR.BSID_ENCBS056AAA.BSREP1.TECHREP1.FILEIDENCFF000QLO.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CEBPB.MCF-7.EXPID_ENCSR000BSR.BSID_ENCBS056AAA.BSREP2.TECHREP1.FILEIDENCFF000QLL.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.MCF-7.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#39 , 2512709958, order: 15, svr: scg, old #: 76
NTH=5; SUFFIX="CHIPseq.CEBPB.GM12878.EXPID_ENCSR000BRX"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CEBPB.GM12878.EXPID_ENCSR000BRX.BSID_ENCBS110ENC.BSREP1.TECHREP1.FILEIDENCFF000NUD.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CEBPB.GM12878.EXPID_ENCSR000BRX.BSID_ENCBS110ENC.BSREP2.TECHREP1.FILEIDENCFF000NUB.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.GM12878.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#40 , 1902788434, order: 15, svr: scg, old #: 160
NTH=3; SUFFIX="CHIPseq.CEBPB.A549.EXPID_ENCSR000DYI"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CEBPB.A549.EXPID_ENCSR000DYI.BSID_ENCBS159AAA.BSREP1.TECHREP1.FILEIDENCFF000VOL.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CEBPB.A549.EXPID_ENCSR000DYI.BSID_ENCBS159AAA.BSREP2.TECHREP1.FILEIDENCFF000VON.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.A549.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.A549/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.A549/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#41 , 1846953227, order: 15, svr: scg, old #: 173
NTH=10; SUFFIX="CHIPseq.CEBPB.K562.EXPID_ENCSR000BRQ"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CEBPB.K562.EXPID_ENCSR000BRQ.BSID_ENCBS109ENC.BSREP1.TECHREP1.FILEIDENCFF000PXH.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CEBPB.K562.EXPID_ENCSR000BRQ.BSID_ENCBS109ENC.BSREP2.TECHREP1.FILEIDENCFF000PXC.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.K562.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.K562/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.K562/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 5000000
##SUBSAMPLED CTL (5M)!
sleep 5
#42 , 1842798337, order: 15, svr: scg, old #: 176
NTH=3; SUFFIX="CHIPseq.CEBPB.K562.EXPID_ENCSR000EHE"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CEBPB.K562.EXPID_ENCSR000EHE.BSID_ENCBS039ENC.BSREP1.TECHREP1.FILEIDENCFF000YIC.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CEBPB.K562.EXPID_ENCSR000EHE.BSID_ENCBS039ENC.BSREP2.TECHREP1.FILEIDENCFF000YID.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.K562.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.K562/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.K562/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#43 , 1840065916, order: 15, svr: scg, old #: 177
NTH=3; SUFFIX="CHIPseq.CEBPB.H1-hESC.EXPID_ENCSR000EBV"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CEBPB.H1-hESC.EXPID_ENCSR000EBV.BSID_ENCBS854AAA.BSREP1.TECHREP1.FILEIDENCFF000WRB.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CEBPB.H1-hESC.EXPID_ENCSR000EBV.BSID_ENCBS854AAA.BSREP2.TECHREP1.FILEIDENCFF000WRD.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.H1-hESC.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.H1-hESC/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.H1-hESC/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#44 , 1747602752, order: 15, svr: scg, old #: 188
NTH=3; SUFFIX="CHIPseq.CEBPB.HeLa-S3.EXPID_ENCSR000EDA"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CEBPB.HeLa-S3.EXPID_ENCSR000EDA.BSID_ENCBS637AAA.BSREP1.TECHREP1.FILEIDENCFF000XBO.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CEBPB.HeLa-S3.EXPID_ENCSR000EDA.BSID_ENCBS637AAA.BSREP2.TECHREP1.FILEIDENCFF000XBN.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HeLa-S3.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HeLa-S3/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HeLa-S3/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#45 , 5217533603, order: 16, svr: scg, old #: 1
NTH=10; SUFFIX="CHIPseq.REST.Panc1.EXPID_ENCSR000BJO"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.REST.Panc1.EXPID_ENCSR000BJO.BSID_ENCBS425ENC.BSREP2.TECHREP1.FILEIDENCFF000QST.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.REST.Panc1.EXPID_ENCSR000BJO.BSID_ENCBS425ENC.BSREP1.TECHREP1.FILEIDENCFF000QSN.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.Panc1.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.Panc1/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.Panc1/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#46 , 4291140408, order: 16, svr: scg, old #: 5
NTH=8; SUFFIX="CHIPseq.REST.HL-60.EXPID_ENCSR000BTF"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.REST.HL-60.EXPID_ENCSR000BTF.BSID_ENCBS070ENC.BSREP2.TECHREP1.FILEIDENCFF000PUO.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.REST.HL-60.EXPID_ENCSR000BTF.BSID_ENCBS070ENC.BSREP1.TECHREP1.FILEIDENCFF000PUD.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HL-60.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HL-60/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HL-60/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#47 , 3379815904, order: 16, svr: scg, old #: 21
NTH=6; SUFFIX="CHIPseq.REST.GM12878.EXPID_ENCSR000BGF"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.REST.GM12878.EXPID_ENCSR000BGF.BSID_ENCBS110ENC.BSREP1.TECHREP1.FILEIDENCFF000NZA.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.REST.GM12878.EXPID_ENCSR000BGF.BSID_ENCBS110ENC.BSREP2.TECHREP1.FILEIDENCFF000NYY.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.GM12878.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#48 , 3379734432, order: 16, svr: scg, old #: 22
NTH=6; SUFFIX="CHIPseq.REST.HepG2.EXPID_ENCSR000BJL"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.REST.HepG2.EXPID_ENCSR000BJL.BSID_ENCBS114ENC.BSREP2.TECHREP1.FILEIDENCFF000PMN.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.REST.HepG2.EXPID_ENCSR000BJL.BSID_ENCBS114ENC.BSREP1.TECHREP1.FILEIDENCFF000PMK.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HepG2.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#49 , 2996888716, order: 16, svr: scg, old #: 43
NTH=5; SUFFIX="CHIPseq.REST.MCF-7.EXPID_ENCSR000BSP"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.REST.MCF-7.EXPID_ENCSR000BSP.BSID_ENCBS056AAA.BSREP1.TECHREP1.FILEIDENCFF000QPH.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.REST.MCF-7.EXPID_ENCSR000BSP.BSID_ENCBS056AAA.BSREP2.TECHREP1.FILEIDENCFF000QPE.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.MCF-7.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#50 , 2785346920, order: 16, svr: scg, old #: 55
NTH=5; SUFFIX="CHIPseq.REST.SK-N-SH.EXPID_ENCSR000BJJ"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.REST.SK-N-SH.EXPID_ENCSR000BJJ.BSID_ENCBS428ENC.BSREP2.TECHREP1.FILEIDENCFF000RAO.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.REST.SK-N-SH.EXPID_ENCSR000BJJ.BSID_ENCBS428ENC.BSREP1.TECHREP1.FILEIDENCFF000RAL.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.SK-N-SH.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.SK-N-SH/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.SK-N-SH/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#51 , 2695678500, order: 16, svr: scg, old #: 61
NTH=5; SUFFIX="CHIPseq.REST.HCT116.EXPID_ENCSR000BVI"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.REST.HCT116.EXPID_ENCSR000BVI.BSID_ENCBS389ENC.BSREP1.TECHREP1.FILEIDENCFF000PAW.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.REST.HCT116.EXPID_ENCSR000BVI.BSID_ENCBS389ENC.BSREP2.TECHREP1.FILEIDENCFF000PAX.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HCT116.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HCT116/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HCT116/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#52 , 2660592200, order: 16, svr: scg, old #: 64
NTH=5; SUFFIX="CHIPseq.REST.HepG2.EXPID_ENCSR000BOT"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.REST.HepG2.EXPID_ENCSR000BOT.BSID_ENCBS114ENC.BSREP2.TECHREP1.FILEIDENCFF000PMV.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.REST.HepG2.EXPID_ENCSR000BOT.BSID_ENCBS114ENC.BSREP1.TECHREP1.FILEIDENCFF000PMU.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HepG2.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#53 , 2367885518, order: 16, svr: scg, old #: 93
NTH=4; SUFFIX="CHIPseq.REST.H1-hESC.EXPID_ENCSR000BHM"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.REST.H1-hESC.EXPID_ENCSR000BHM.BSID_ENCBS111ENC.BSREP2.TECHREP1.FILEIDENCFF000OQY.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.REST.H1-hESC.EXPID_ENCSR000BHM.BSID_ENCBS111ENC.BSREP1.TECHREP1.FILEIDENCFF000OQQ.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.H1-hESC.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.H1-hESC/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.H1-hESC/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#54 , 2137110021, order: 16, svr: scg, old #: 119
NTH=4; SUFFIX="CHIPseq.REST.SK-N-SH.EXPID_ENCSR000BOZ"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.REST.SK-N-SH.EXPID_ENCSR000BOZ.BSID_ENCBS428ENC.BSREP2.TECHREP1.FILEIDENCFF000RAW.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.REST.SK-N-SH.EXPID_ENCSR000BOZ.BSID_ENCBS428ENC.BSREP1.TECHREP1.FILEIDENCFF000RAT.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.SK-N-SH.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.SK-N-SH/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.SK-N-SH/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#55 , 1965762041, order: 16, svr: scg, old #: 148
NTH=3; SUFFIX="CHIPseq.REST.Panc1.EXPID_ENCSR000BUP"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.REST.Panc1.EXPID_ENCSR000BUP.BSID_ENCBS425ENC.BSREP2.TECHREP1.FILEIDENCFF000QTD.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.REST.Panc1.EXPID_ENCSR000BUP.BSID_ENCBS425ENC.BSREP1.TECHREP1.FILEIDENCFF000QTA.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.Panc1.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.Panc1/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.Panc1/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#56 , 1948675408, order: 16, svr: scg, old #: 152
NTH=3; SUFFIX="CHIPseq.REST.HeLa-S3.EXPID_ENCSR000BMN"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.REST.HeLa-S3.EXPID_ENCSR000BMN.BSID_ENCBS113ENC.BSREP1.TECHREP1.FILEIDENCFF000PEQ.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.REST.HeLa-S3.EXPID_ENCSR000BMN.BSID_ENCBS113ENC.BSREP2.TECHREP1.FILEIDENCFF000PEM.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HeLa-S3.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HeLa-S3/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HeLa-S3/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#57 , 1902737624, order: 16, svr: scg, old #: 161
NTH=15; SUFFIX="CHIPseq.REST.K562.EXPID_ENCSR000BMW"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.REST.K562.EXPID_ENCSR000BMW.BSID_ENCBS109ENC.BSREP1.TECHREP1.FILEIDENCFF000QCX.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.REST.K562.EXPID_ENCSR000BMW.BSID_ENCBS109ENC.BSREP2.TECHREP1.FILEIDENCFF000QCW.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.K562.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.K562/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.K562/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 10000000
##SUBSAMPLED CTL (10M)!
sleep 5
#58 , 3577006545, order: 17, svr: scg, old #: 13
NTH=7; SUFFIX="CHIPseq.MAX.HepG2.EXPID_ENCSR000BTM"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.MAX.HepG2.EXPID_ENCSR000BTM.BSID_ENCBS114ENC.BSREP2.TECHREP1.FILEIDENCFF000PKZ.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.MAX.HepG2.EXPID_ENCSR000BTM.BSID_ENCBS114ENC.BSREP1.TECHREP1.FILEIDENCFF000PKX.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HepG2.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#59 , 3413829269, order: 17, svr: scg, old #: 20
NTH=6; SUFFIX="CHIPseq.MAX.A549.EXPID_ENCSR000BTJ"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.MAX.A549.EXPID_ENCSR000BTJ.BSID_ENCBS164AAA.BSREP2.TECHREP1.FILEIDENCFF000NDT.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.MAX.A549.EXPID_ENCSR000BTJ.BSID_ENCBS164AAA.BSREP1.TECHREP1.FILEIDENCFF000NDP.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.A549.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.A549/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.A549/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#60 , 3281945458, order: 17, svr: scg, old #: 26
NTH=6; SUFFIX="CHIPseq.MAX.HCT116.EXPID_ENCSR000BSH"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.MAX.HCT116.EXPID_ENCSR000BSH.BSID_ENCBS389ENC.BSREP2.TECHREP1.FILEIDENCFF000PAQ.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.MAX.HCT116.EXPID_ENCSR000BSH.BSID_ENCBS389ENC.BSREP1.TECHREP1.FILEIDENCFF000PAP.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HCT116.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HCT116/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HCT116/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
########### scg3 (QLOGIN)
#61 , 3096155876, order: 17, svr: scg, old #: 32
NTH=6; SUFFIX="CHIPseq.MAX.H1-hESC.EXPID_ENCSR000BSJ"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.MAX.H1-hESC.EXPID_ENCSR000BSJ.BSID_ENCBS111ENC.BSREP2.TECHREP1.FILEIDENCFF000OQD.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.MAX.H1-hESC.EXPID_ENCSR000BSJ.BSID_ENCBS111ENC.BSREP1.TECHREP1.FILEIDENCFF000OQI.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.H1-hESC.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.H1-hESC/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.H1-hESC/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#62 , 2984564336, order: 17, svr: scg, old #: 44
NTH=5; SUFFIX="CHIPseq.MAX.MCF-7.EXPID_ENCSR000BUL"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.MAX.MCF-7.EXPID_ENCSR000BUL.BSID_ENCBS056AAA.BSREP1.TECHREP1.FILEIDENCFF000QOS.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.MAX.MCF-7.EXPID_ENCSR000BUL.BSID_ENCBS056AAA.BSREP2.TECHREP1.FILEIDENCFF000QON.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.MCF-7.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#63 , 2742356844, order: 17, svr: scg, old #: 58
NTH=5; SUFFIX="CHIPseq.MAX.SK-N-SH.EXPID_ENCSR000BVD"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.MAX.SK-N-SH.EXPID_ENCSR000BVD.BSID_ENCBS428ENC.BSREP2.TECHREP1.FILEIDENCFF000QZQ.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.MAX.SK-N-SH.EXPID_ENCSR000BVD.BSID_ENCBS428ENC.BSREP1.TECHREP1.FILEIDENCFF000QZN.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.SK-N-SH.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.SK-N-SH/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.SK-N-SH/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#64 , 2359401285, order: 17, svr: scg, old #: 95
NTH=4; SUFFIX="CHIPseq.MAX.NB4.EXPID_ENCSR000EHS"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.MAX.NB4.EXPID_ENCSR000EHS.BSID_ENCBS259AAA.BSREP2.TECHREP1.FILEIDENCFF000ZMP.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.MAX.NB4.EXPID_ENCSR000EHS.BSID_ENCBS259AAA.BSREP1.TECHREP1.FILEIDENCFF000ZMN.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.NB4.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.NB4/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.NB4/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out
sleep 5
#65 , 2191587951, order: 17, svr: scg, old #: 110
NTH=4; SUFFIX="CHIPseq.MAX.A549.EXPID_ENCSR000DYG"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.MAX.A549.EXPID_ENCSR000DYG.BSID_ENCBS159AAA.BSREP1.TECHREP1.FILEIDENCFF000VPS.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.MAX.A549.EXPID_ENCSR000DYG.BSID_ENCBS159AAA.BSREP2.TECHREP1.FILEIDENCFF000VPU.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.A549.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.A549/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.A549/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#66 , 2080172525, order: 17, svr: scg, old #: 134
NTH=4; SUFFIX="CHIPseq.MAX.K562.EXPID_ENCSR000BLP"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.MAX.K562.EXPID_ENCSR000BLP.BSID_ENCBS109ENC.BSREP2.TECHREP1.FILEIDENCFF000QCC.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.MAX.K562.EXPID_ENCSR000BLP.BSID_ENCBS109ENC.BSREP1.TECHREP1.FILEIDENCFF000QBZ.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.K562.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.K562/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.K562/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#67 , 1890241158, order: 17, svr: scg, old #: 165
NTH=3; SUFFIX="CHIPseq.MAX.GM12878.EXPID_ENCSR000DZF"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.MAX.GM12878.EXPID_ENCSR000DZF.BSID_ENCBS630AAA.BSREP2.TECHREP1.FILEIDENCFF000VYA.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.MAX.GM12878.EXPID_ENCSR000DZF.BSID_ENCBS630AAA.BSREP1.TECHREP1.FILEIDENCFF000VXY.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.GM12878.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.GM12878/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#68 , 1762383064, order: 17, svr: scg, old #: 186
NTH=3; SUFFIX="CHIPseq.MAX.HeLa-S3.EXPID_ENCSR000ECN"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.MAX.HeLa-S3.EXPID_ENCSR000ECN.BSID_ENCBS637AAA.BSREP1.TECHREP1.FILEIDENCFF000XHD.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.MAX.HeLa-S3.EXPID_ENCSR000ECN.BSID_ENCBS637AAA.BSREP2.TECHREP1.FILEIDENCFF000XHF.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HeLa-S3.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HeLa-S3/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HeLa-S3/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#69 , 4447348119, order: 18, svr: scg, old #: 3
NTH=8; SUFFIX="CHIPseq.CTCF.H1-hESC.EXPID_ENCSR000BNH"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CTCF.H1-hESC.EXPID_ENCSR000BNH.BSID_ENCBS111ENC.BSREP2.TECHREP1.FILEIDENCFF000OOF.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CTCF.H1-hESC.EXPID_ENCSR000BNH.BSID_ENCBS111ENC.BSREP1.TECHREP1.FILEIDENCFF000ONR.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.H1-hESC.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.H1-hESC/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.H1-hESC/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#70 , 3252094990, order: 18, svr: scg, old #: 28
NTH=6; SUFFIX="CHIPseq.CTCF.MCF-7.EXPID_ENCSR000AHD"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CTCF.MCF-7.EXPID_ENCSR000AHD.BSID_ENCBS000AAA.BSREP1.TECHREP1.FILEIDENCFF000QLW.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CTCF.MCF-7.EXPID_ENCSR000AHD.BSID_ENCBS001AAA.BSREP2.TECHREP1.FILEIDENCFF000QLT.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.MCF-7.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#71 , 2679120397, order: 18, svr: scg, old #: 62
NTH=5; SUFFIX="CHIPseq.CTCF.A549.EXPID_ENCSR000DNA"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CTCF.A549.EXPID_ENCSR000DNA.BSID_ENCBS162AAA.BSREP2.TECHREP1.FILEIDENCFF000RMC.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CTCF.A549.EXPID_ENCSR000DNA.BSID_ENCBS162AAA.BSREP1.TECHREP1.FILEIDENCFF000RMB.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.A549.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.A549/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.A549/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#72 , 2561792780, order: 18, svr: scg, old #: 71
NTH=5; SUFFIX="CHIPseq.CTCF.HepG2.EXPID_ENCSR000BIE"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CTCF.HepG2.EXPID_ENCSR000BIE.BSID_ENCBS114ENC.BSREP1.TECHREP1.FILEIDENCFF000PHG.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CTCF.HepG2.EXPID_ENCSR000BIE.BSID_ENCBS114ENC.BSREP2.TECHREP1.FILEIDENCFF000PHE.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HepG2.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HepG2/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#73 , 2525048883, order: 18, svr: scg, old #: 73
NTH=5; SUFFIX="CHIPseq.CTCF.MCF-7.EXPID_ENCSR000DMR"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CTCF.MCF-7.EXPID_ENCSR000DMR.BSID_ENCBS017ENC.BSREP1.TECHREP1.FILEIDENCFF000SAY.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CTCF.MCF-7.EXPID_ENCSR000DMR.BSID_ENCBS017ENC.BSREP2.TECHREP1.FILEIDENCFF000SAX.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.MCF-7.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#74 , 2483146438, order: 18, svr: scg, old #: 78
NTH=4; SUFFIX="CHIPseq.CTCF.MCF-7.EXPID_ENCSR000DML"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CTCF.MCF-7.EXPID_ENCSR000DML.BSID_ENCBS251AAA.BSREP2.TECHREP1.FILEIDENCFF000SAP.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CTCF.MCF-7.EXPID_ENCSR000DML.BSID_ENCBS251AAA.BSREP1.TECHREP1.FILEIDENCFF000SAO.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.MCF-7.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#75 , 2457028026, order: 18, svr: scg, old #: 80
NTH=4; SUFFIX="CHIPseq.CTCF.K562.EXPID_ENCSR000EGM"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CTCF.K562.EXPID_ENCSR000EGM.BSID_ENCBS039ENC.BSREP1.TECHREP1.FILEIDENCFF000YLW.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CTCF.K562.EXPID_ENCSR000EGM.BSID_ENCBS039ENC.BSREP2.TECHREP1.FILEIDENCFF000YLY.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.K562.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.K562/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.K562/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
#76 , 2423703449, order: 18, svr: scg, old #: 84
NTH=4; SUFFIX="CHIPseq.CTCF.MCF-7.EXPID_ENCSR000DMO"
FASTQ1=$DATA/DREAM_challenge/CHIPseq.CTCF.MCF-7.EXPID_ENCSR000DMO.BSID_ENCBS252AAA.BSREP2.TECHREP1.FILEIDENCFF000SAL.unpaired.fastq.gz
FASTQ2=$DATA/DREAM_challenge/CHIPseq.CTCF.MCF-7.EXPID_ENCSR000DMO.BSID_ENCBS252AAA.BSREP1.TECHREP1.FILEIDENCFF000SAK.unpaired.fastq.gz
CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.MCF-7.unpaired.fastq.gz
WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/align/rep1 ctl1
cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.MCF-7/out/qc/rep1 ctl1
cd $WORK;
bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -fastq2 $FASTQ2 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out -subsample_ctl 40000000
##SUBSAMPLED CTL (40M)!
sleep 5
# in CTCF_blacklist.txt
#77 , 2370598870, order: 18, svr: scg, old #: 92
#NTH=4; SUFFIX="CHIPseq.CTCF.HEK293.EXPID_ENCSR000DTW"
#FASTQ1=$DATA/DREAM_challenge/CHIPseq.CTCF.HEK293.EXPID_ENCSR000DTW.BSID_ENCBS393ENC.BSREP1.TECHREP1.FILEIDENCFF001HNG.unpaired.fastq.gz
#CTL_FASTQ=$DATA/DREAM_challenge/CONTROL.HEK293.unpaired.fastq.gz
#WORK=$RUN/DREAM_challenge/$SUFFIX; mkdir -p $WORK/out/align; mkdir -p $WORK/out/qc
#cd $WORK/out/align; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HEK293/out/align/rep1 ctl1
#cd $WORK/out/qc; rm ctl1; ln -s ../../../../DREAM_challenge_ctl/CONTROL.HEK293/out/qc/rep1 ctl1
#cd $WORK;
#bds_scr_5min ${SUFFIX//\//_} $CODE/bds_atac/chipseq/chipseq.bds -bw_for_pooled_rep_only -no_naive_overlap -species hg19 -nth $NTH -fastq1 $FASTQ1 -ctl_fastq $CTL_FASTQ -title ${SUFFIX//\//_} -url_base http://mitra.stanford.edu/kundaje/leepc12/DREAM_challenge/$SUFFIX/out
#sleep 5
#78 , 2220479962, order: 18, svr: scg, old #: 107