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databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
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columns in ref_peaks_coverage.bed #233

Open cristanchoa opened 1 year ago

cristanchoa commented 1 year ago

Hi,

Thanks for the package! I am having trouble running the pipeline again with the reference peaks - potentially due to the glitch in not having Rutils mentioned in #229 affecting the looper runp function

However, I do see that in the individual samples there is now a "ref_peaks_coverage.bed" file. I don't see a separate "ref.narrowpeaks" file. What are the columns in this file? When I pull it into R I get the following:

image

The glossary for this kind of file only mentions 4 columns for this kind of file. Here is V5 the counts? While the pipeline is fixed, is it reasonable to pull these count values into a table for downstream analysis?

Thanks so much!

lucasrocmoreira commented 2 weeks ago

Hi,

I would also like to know the answer to this question. I couldn't find anywhere.

Thanks, Lucas