Help pls! Data normalization for ChIP-seq under different conditions

[lavagirl]

Hi guys,

This may be a really naive question for you, but I have no ChIPseq or bioinformatic experience at all.

I have done chipseq with the same antibody in fly but under two different conditions. For each condition, I've done peak calling (MACS) using input control. Then how do i normalize these two datasets? Apparently one dataset has more reads than the other. i did some literature research. Some people said "using library size". Some other said "using mean coverage". Don't really understand how i could do it. Is there any program i can use?

Thank you so much for great patience and help!!!

[dawe]

Try this http://genomebiology.com/content/pdf...2-13-3-r16.pdf.
Anyway, macs2 has options to scale one sample to the other if the number of reads is larger

d

[lavagirl]

I see. Thank you so much!

Try this http://genomebiology.com/content/pdf...2-13-3-r16.pdf.
Anyway, macs2 has options to scale one sample to the other if the number of reads is larger

d