Entering edit mode
9.4 years ago
jack
▴
980
Hi,
I have read files from Chip-seq experiments for both control and treatment samples. I want to do peak calling, so when I was creating .bam files, only small percentage of the reads from control sample are mapped to genome which seem for me bit strange.
Does anybody knows why?
We'd need to see the data man - there are 100 reasons why your reads might not map :)
When you say control sample, do you mean "input", like sequenced with no antibody pulldown - just the chromatin?
Any possible of the contamination issue? In addition, how about the quailty of reads you have?
What do you consider a small percentage? What, specifically, is the nature of the control? What genome?
Try to blast a few and see what organism then end up in.