TADs are 3D structural units of higher-order chromosome organization in Drosophila

Quentin Szabo et al. ,TADs are 3D structural units of higher-order chromosome organization in Drosophila.Sci. Adv.4,eaar8082(2018).DOI:10.1126/sciadv.aar8082

Members

• Hoe Zi Onn, 111753229
• Han-Cheng Guan, 112753134
• Hao-Yun Hsieh, 112753120

Demo

To use our pre-configured environment for the first time (assuming you have git & docker installed):

git clone /~https://github.com/1121-NCCUBionf/finalproject-group1.git
cd finalproject-group1
docker volume create project-data
docker build -t project-env .
docker run -v project-data:/project-data -it project-env

• store your data in project-data docker volume
• and you can access your data in /project-data directory inside the container

Folder organization and its related information

docs/

• Our presentation, 1121_bioinformatics_FP_group1.pdf
• Any related document for the project
  • A note for the development

data/

downloadable data are not included in this repository see here for more information.

Data	Source	Format	Size	Description
Raw Data	NCBI GSE99107	fastq	~ 250 GB (compressed)	6 samples
Reference Genome	UCSC dm6	fasta	147 MB	2014
Genome Index	from bowtie2	bt2	-	-

code/

• Packages we use
  • original packages in the paper
    • None
  • additional packages we found
    • fanc
    • bowtie2
    • fastqsplitter
    • (sambamba)
• scripts
  • for downloading raw fastq data
  • for running fanc example pipeline
  • for running fanc pipeline with our data
  • for splitting fastq files into smaller chunks
  • handy Makefile to copy file between host and container

results/

• Which part of the paper do we reproduce?
  • Hi-C data processing
  • Hi-C contact map visualization
• Improvement or change in our package?
  • we use dm6 genome instead of dm3

References

• see packages/tools we use here.