Question: Normalization with deepTools
gravatar for Lorenzo
13 days ago by
Lorenzo0 wrote:

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!

rna-seq • 78 views
ADD COMMENTlink modified 13 days ago by Friederike6.5k • written 13 days ago by Lorenzo0
gravatar for Friederike
13 days ago by
United States
Friederike6.5k wrote:

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

ADD COMMENTlink written 13 days ago by Friederike6.5k
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