How to normalize Bigwig files to per million reads?
This may sound stupid but I am new to this. I have got Bigwig files for ChIP-seq data for PolII for different treatments. But each sample had different total reads so I want to get normalized Bigwig file (probably per million reads normalization) so that its easy to compare the signal on IGV.
Thanks!
1 answer
Well technically this needs to be done before you convert.
What you can do is round trip the data into bedgraph where you can normalize the value with a simple awk script then convert it back to bigwig.
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Istvan Albert
You have to download the tools from http://hgdownload.cse.ucsc.edu/admin/exe/ for your platform, then use bigWigtoBedgGraph and bedGraphtoBigWig pairs.
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Ram
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Istvan Albert
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