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