Hello everyone! Sorry for long explanation!
I did paired-end ChIP-seq for my input and IP samples and I used MNase instead of sonication for DNA fragmentation. I have duplicate of each sample. After converting from fastq. to sam files, I merged duplicates of each sample with bamtools and also sorted bam files (just to compress files). Then I imported these bam files to galaxy and tried to perform peak calling with the default setting using MACS2 callpeak. I got 82000 regions from narrowpeaks but based on the transcription factor binding sites that I am looking for, I should not have more than 35000 binding sites. I tried to do change settings for MACS2 callpeak as follows and I got 62000 regions:
Band width for picking regions to compute fragment size 500 Set lower mfold bound 150 Set upper mfold bound 1000 Set extension size 100
So the question is if this method of analysis is ok for my special samples regarding using MNase and also a paired-end seq? Do you have any suggestion to optimise the analysis?
Thanks and hope to have your suggestions !