Normalization of ChIP-Seq count matrix ??
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
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