I was hoping someone could point me in the right direction for MNase-seq analysis. I just recently got my hands on a dataset, and after a great deal of looking around, I'm having trouble finding a proper protocol.
Could I get a general outline? I know some sequencing types don't like having their fastq files filtered because it messes with downstream analysis and that sort of thing.
So something like:
1) Filter fastq
2) Map to genome using bowtie2
3) Filter sam/bam for duplicates, trim reads
4) call peaks with macs2
and so on. I am attempting to identify nucleosome positions in mm9 genome but would like to read a few papers that go over the most commonly used tools for mapping and peak calling and so forth.