How to get Read Counts from MACS2 output files?
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14 months ago
cthangav ▴ 40

Hello, I am working with GEO datasets that supply both bigwig(bw) and bed files for each ATAC sample. I need the read counts/pile up value for downstream analysis, but the 6+4 narrow peak file format from MACS2 does not include the read counts. Is it possible to get read counts from bigwig files? Or is the only way to get the counts to go the the raw data, realign, de-blacklist, and run MACS2 again?

ATAC-seq pileup narrowpeak readcounts MACS2 • 359 views

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