This is a test version of Biostars. For the public version, visit https://www.biostars.org.
normalization of ChIP-seq data

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

chip-seq normalization
• 2,005 views • link
updated by Devon Ryan Devon Ryan • written by Bogdan Bogdan

1 answer

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

• 0 views • link
written by Devon Ryan Devon Ryan

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

• 0 views • link
written by Bogdan Bogdan

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).

• 0 views • link
written by Devon Ryan Devon Ryan

Log in to answer this question.

More posts like this