call peaks of single-end mapping bam files

Question

[szp770]

Hi, for certain reasons, I need to map double-end sequencing result seperately, for example, I mapped A_R1.fastq to A_R1.bam, and A_R2.fastq to A_R2.bam, now I want to call peaks of this file, how can I call peaks of these two files? Do I need to merge them and call peaks?

[Nitin Narwade]

for certain reasons, I need to map double-end sequencing result seperately

What are the reasons to align R1 and R2 seperately??

And if you are aligning them seperately and has some reason to process them as a single end sequencing reads then why would you merge them?

I hope this will help you to think in a right way.

Thanks, Nitin

[szp770]

Now I am analysing hichip data, a software needs to map the reads seperately and then use the two mapped bam files to generate a matrix, this is for the software. But I also need to call peaks from the bam files, so I don't know how to call peak for the seperately mapping files.