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fix: read quantification #22

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merged 5 commits into from
Jun 19, 2024
Merged

fix: read quantification #22

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e4e9217
fix: start salmon in --ont mode
yeising Jun 10, 2024
30179de
fix: samtools creates BAM files without sorting for salmon
yeising Jun 11, 2024
ec99cb4
feat: create transcriptome from genome.fa and annotation.gff
yeising Jun 13, 2024
abd4d45
fix: resources and linting
yeising Jun 17, 2024
e7cd137
fix: removed obsolete comment
yeising Jun 19, 2024
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4 changes: 2 additions & 2 deletions workflow/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -129,7 +129,7 @@ rule sam_stats:

rule count_reads:
input:
bam=rules.sam_index.output.ibam,
bam=rules.map_reads.output, # use unsorted .bam files; minimap2 does not create .bam -> new input needed; also filtering may be necessary (cutadapt)
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Please update the comment: Just state that compressed output will not be generated. The filtering is some kind of TODO, which we ought to discuss

trs=config["transcriptome"],
output:
tsv="counts/{sample}_salmon/quant.sf",
Expand All @@ -142,7 +142,7 @@ rule count_reads:
"envs/env.yml"
shell:
"""
salmon --no-version-check quant -p {resources.cpus_per_task} \
salmon --no-version-check quant --ont -p {resources.cpus_per_task} \
-t {input.trs} -l {params.libtype} -a {input.bam} -o {params.tsv_dir} &> {log}
"""

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