Question

Read counts for peak file

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3.2 years ago

Romylland ▴ 10

Hi,

Need some help. I need a peak call file with read counts for some downstream analysis. I have my BAM file, I used MACS2 to get the peak calls, next I used Samtools bedcov but I am not familiar with these tools therefore I don't know bedcov output header to identify the reads count if any. How may I get the reads count falling between the position coordinate?

RNA-Seq alignment • 2.1k views

ADD COMMENT • link updated 2.4 years ago by Farzaneh • 0 • written 3.2 years ago by Romylland ▴ 10

score 3 · Answer 1 · 2021-01-26

3

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3.2 years ago

ATpoint 82k

You can make a SAF file out of that narrowPeak file from macs, see Converting from BED to SAF/GFF and then use featureCounts from the subread package to get the count matrix:

featureCounts -a in.saf -F SAF -o out.counts your.bam

ADD COMMENT • link 3.2 years ago by ATpoint 82k

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Thanks a lot. Will give it a try now and keep u posted :)

ADD REPLY • link 3.2 years ago by Romylland ▴ 10

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Was successful, thanks you for your support. Still got one last question the last column of featureCounts output I guess is my read counts, right? Thanks [ATpoint]