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...