Question: why only small fraction of reads from control sample of chip-seq are mapping into the genome ?
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gravatar for jack
3.8 years ago by
jack750
Germany
jack750 wrote:

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? 

chip-seq • 1.3k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by jack750

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?

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by John12k

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

ADD REPLYlink written 3.8 years ago by Gary450

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

ADD REPLYlink written 3.8 years ago by bede.portz470

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

ADD REPLYlink written 3.8 years ago by Devon Ryan89k
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