MACS2 Total Reads Within a Peak?

Question

[takamichael]

Hi,

I wanted to know if there is a way to determine the number of TOTAL reads within a peak being called by the MACS2 command callpeaks?

I am aware that it gives the pileup of reads for the summit peak but I want to know the total reads for each peak being outputted.

P.S I have already tried coveragebed from bedtools.

Thank you!

[Pierre Lindenbaum]

P.S I have already tried coveragebed from bedtools.

and ?

[takamichael]

I am not seeing the total reads in the .cnt.bed file I just get the following information.

chr4 93874012 93874062 HWI-ST926:425:C5WF1ACXX:4:1101:1118:1982 60 - 93874012 93874062 0,0,0 1 50, 0, 0