sequencing of control sample in ChIP-seq??

Question

[woongjaej]

Hi guys,

I'm trying to analysis ChIP-seq data and have a question about control sample.

First, I sequenced my samples about 2 G bases to check the quality of the samples and libraries.

I have verified samples' qualities and decided to sequence deeper for these samples.

Assuming that I will read about 10G bases more for these samples, here's my question.

Should I read 10G bases for control sample(Input) more just like other ChIP samples?? Can't I just use 2G base control sample data??

(ex. control sample = 2G, treat sample = 10G -->>possible or impossible??)

If I should read 10G bases for control sample just like other treat samples, could somebody tell me why???

Thank you very much...

Answer 1

[Devon Ryan]

It's generally best to sequence the control samples at least as deeply as the IPs. If you don't do this, the IP samples will just get scaled down during peak calling, which will partially remove the benefit of increased depth.

[woongjaej]

Thank Ryan for kind reply!!