I am trying to use macs1.4 for peak calling with my alignment file which is in .sam format. This is a medip sequencing data. However I am facing an issue. 1. While I am using the trimmed and aligned file (.sam format) I am getting 258939 no of peaks.
- Afterwards I have converted the sam file to a bam file sorted them, filtered unmapped reads and again did run run macs on trimmed,aligned,sorted and filtered reads file (.sam format) and agin getting same no. of peaks i.e 258939
this is confusing. since the no of peaks are exactly same even after the filtering unmapped reads. Hope to get some response..
Thanking in advance,