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Understanding bamCoverage output

Open Zepeng-Mu opened this issue 2 years ago • 0 comments

Hello,

I used bamCoverage with RPKM normalization to get bigwig files. I then used pyBigWig.values() function to view bigwig files in a given genomic region. I noticed all the non-zero entries in the bigwig are integers. I'm worried that these integers are not normalized values but just raw read counts pile up?

My question is can I safely use pyBigWig.values() to extract normalized bigwig values for each bp in the region that I'm interested in?

Thanks so much!

Zepeng-Mu avatar Oct 14 '22 17:10 Zepeng-Mu