How to normalize Bigwig files to per million reads?

Question

[KB]

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!

Answer 1

[Istvan Albert]

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.

[KB]

Thanks Istvan. I have BAM, SAM, Bedgraph, Bigwig files but no idea how exactly to do that. Can you please detail?

[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.