MACS peak calling of paired-end reads in SAM format

Question

[biostart]

HI,

Just a quick question: if SAM format is used for paired-end reads, will these be automatically recognised as paired-end by MACS when doing peak-calling?

Thanks!

Answer 1

[ATpoint]

MACS was developed in the days of short single-end reads. As far as I know, it can autodetect the file type (SAM, BAM, BED, Eland...), but you have to indicate if paired-end reads are present of not. I would write your SAM files as BAM (samtools view -b in.sam -o out.bam), and then add to your command -f BAMPE. You can also check from the stuff MACS writes to STDERR if MACS says "read treatment tags" (indicating single end) or "read treatment fragments" (indicating paired-reads, because two reads are read that are sequenced from one fragment).