MACS for a paired-end sequencing

Question

[KT]

Hello, I need some help with peak calling with MACS for a paired-end sequencing generated fastq files. I have separate R1/R2 .bam files and would like to know the best way to proceed further.

Answer 1

[Prakash]

If it is paired-end fastq file then why you have separate bam files?. The best would be to realign the paired-end data and you will have one bam file and that can be used for peak calling.

[ATpoint]

Agreed. PE data have to be mapped together otherwise the advantage of the method is gone and you would be double-counting every read. Once you have a paired-end BAM file just use -f BAMPE as parameter in macs. It will take care of the rest.

[KT]

Thank you very much for suggestion. I will try that and update accordingly.