Normalization with deepTools

Question

[Lorenzo]

Good morning,

I'm doing RNA-seq analysis. I have .bam files coming from 31 different tissues. My goal is to normalize these data in order to obtain .bigwig files and compare them on IGV. Can I use bamCoverage (from deepTools) to do that? If yes, how can I do it?

Thank you in advance for your time and suggestion!

Answer 1

[Friederike]

You can read the details laid out by ATpoint about how to use a scale factor with deepTools. He specified it for ATAC-seq/ChIP-seq, but the principles are the same for RNA-seq: calculate a scaling factor with DESeq2 and supply the inverse (!) to bamCoverage --scaleFactor.

Some more details of the different normalization methods of bamCoverage can be found in this post and perhaps even in thus github issue