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crazyhottommy / pyflow-ChIPseq

a snakemake pipeline to process ChIP-seq files from GEO or in-house
MIT License
101 stars 39 forks source link

Why Downsample? #1

Closed amirshams84 closed 5 years ago

amirshams84 commented 5 years ago

Hi Ming It would be great if you let me know why downsample

crazyhottommy commented 5 years ago

Hi, When you sequence a lot of samples and they do not have the same sequencing depth, you want to downsample them to the same read depth. see method in this paper https://www.nature.com/articles/nature14248 if you do not want to downsample, just set https://github.com/crazyhottommy/pyflow-ChIPseq/blob/master/config.yaml#L15 to a big number.

amirshams84 commented 5 years ago

don't you think it will decrease the diversity and richness of the samples aka sensitivity

crazyhottommy commented 5 years ago

it will decrease the richness of course. but when you do downstream analysis say chromHMM which needs data from all different histone modifications, you want samples to have similar read depth. It depends on what you want to do.

amirshams84 commented 5 years ago

Got It thanks

crazyhottommy commented 5 years ago

close now and you can open when you have other questions.