Hi everyone,
I created a count matrix for ChIP-seq data. Basically I counted the reads present inside peak coordinates and made a matrix. Now I have two questions:
Q1. Do I need to normalise count matrix for library size in order to compare among replicates? If yes, can I use similar strategy like RNA-Seq count normalisation implemented in DESeq2/ edgeR?
Q2. Do I need to take care of normalisation by input counts? I think not because peaks are called on the background of input. So Ican use only direct matrix after library size normalisation.
Please suggest something
Thank you
1 answer
The csaw book discusses ChIP-seq normalization extensively. http://bioconductor.org/books/3.13/csawBook/chap-norm.html
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