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!
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written
by
Lorenzo •
1 answer
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
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