ChIP-Seq Read Counts

Question

[druggable]

Hi Everyone,

I am very new to ChIP-Seq analysis, but i will be analyzing data from multiple studies. However, some ChIP seq studies do not have Input to compare the distribution of mapped reads, so I cannot do peak calling. In this case, is it common practice to simply get the normalized counts (like number of reads relative to library size) for each locus/gene and then compare these values?

Thank you very much.

teabonng

Answer 1

[ATpoint]

You can call peaks withput input control. MACS has that option, trying to assess the background by a local lambda, check the priginal paper for details.