normalization of ChIP-seq data

Question

[Bogdan]

Dear all,

please may I ask about your suggestions regarding the packages/methods that I could use for ChIP-seq normalization (shall I compare two ChIP-seq datasets : before_treatment, and after_treatment). thanks a lot !

-- bogdan

Answer 1

[Devon Ryan]

Assuming you have inputs then SES normalization with bamCompare in deepTools tends to work well.

[Bogdan]

Hi Devon, thank you. We do not have input DNA.

[Devon Ryan]

Then about the best you can do is 1X normalization of each sample and then either subtract them or take the log2 ratio (bamCoverage and bigwigCompare will do that for you).