Get the count.matrix from Chip-Seq BAM files

Question

[elb]

Hi guys, is there a way to get the count matrix from BWA-BAM files of a Chip experiment? Normally this is the standard pipeline in RNA-Seq but this is the first time my boss asked me to do this for Chip-Seq data. normally I run MACS and then I go on. I tried using featureCounts but as far as I know I have to specify the GTF.featureType (eg. exon). How if I don't want to specify the type of feature? Thank you in advance

Answer 1

[ATpoint]

featureCounts accepts the SAF format:

awk 'OFS="\t" {print $1"_"$2"_"$3, $1, $2, $3, "."}' in.narrowPeak > out.saf

The first column is a name column, I simply use a concatenation of chr_start_end. This can go into featureCounts with -F SAF.

[elb]

Okk I'm getting the point. Is it equal with the *broad_peaks.bed file (as from MACS) instead of narrowPeak to generate the SAF file? I suspect yes but I'm not sure. The coordinates (i.e. start-end) should be the same.

[ATpoint]

SAF is Name-Chr-Start-End-Strand

[elb]

Yes, sure! thank you very much!