why only small fraction of reads from control sample of chip-seq are mapping into the genome ?

Question

[jack]

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?

[John]

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?

[Gary]

Any possible of the contamination issue? In addition, how about the quailty of reads you have?

[bede.portz]

What do you consider a small percentage? What, specifically, is the nature of the control? What genome?

[Devon Ryan]

Try to blast a few and see what organism then end up in.