Question: Read counts for peak file
0
gravatar for Romylland
29 days ago by
Romylland0
Romylland0 wrote:

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 • 93 views
ADD COMMENTlink modified 29 days ago by ATpoint45k • written 29 days ago by Romylland0
1
gravatar for ATpoint
29 days ago by
ATpoint45k
ATpoint45k wrote:

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 COMMENTlink written 29 days ago by ATpoint45k

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

ADD REPLYlink written 29 days ago by Romylland0

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]

ADD REPLYlink written 29 days ago by Romylland0

Yep, that is correct.

ADD REPLYlink written 28 days ago by ATpoint45k
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