Hi Catheryn, for ChIP-seq analysis, normalisation and BAM file correlation we use deeptTools. Here you can read more about it: https://github.com/fidelram/deepTools And here is the toolshed repository: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools Cheers, Bjoern

Dear Galaxy,

I am trying to analyze my ChIP-Seq data from Illumina using Galaxy. I have 2 datasets that I want to compare after normalizing each of them to their respective inputs, and these 2 datasets have very different number of reads to start with, is there a way to first normalize each dataset to total number of reads in Galaxy?

Thanks. Your help is very much appreciated.

Catheryn

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