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KoesGroup / Snakemake_ChIPseq_PE

Pipeline for the analysis of PE ChIP-seq data
Creative Commons Attribution Share Alike 4.0 International
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bedgraph -bga #4

Closed mgalland closed 6 years ago

mgalland commented 6 years ago

Hello Jihed, About the pull request #3: Why do you want to report regions with zero coverage (bedtools genomecov -bga)? Is there a specific reason? Because this will significantly increase the size of your bedgraph files. I think you could simply use the -bgoption there and only report the positions with some coverage. Hope it helps, Cheers Marc

JihedC commented 6 years ago

Hi Marc, I didn't give it so much thought to be honest. As I would like to see also coldspot of recombination I thought that if I can observe some locations showing significantly more 0 coverage than others it would be interesting. But I am not sure this is what I get with -bga

mgalland commented 6 years ago

Ok. Let's discuss it and maybe update the Snakefile accordingly.