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Read counts for peak file

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
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updated by Farzaneh • Farzaneh • written by Romylland • Romylland

1 answer

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
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written by ATpoint ATpoint

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

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written by Romylland • Romylland

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]

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written by Romylland • Romylland

Yep, that is correct.

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written by ATpoint ATpoint

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