Choose proper normalization method making bigWig files

[dahun73]

Hello!

I have a question about making bigWig files using bamCoverage. When I make bigWig files, all the samples have different mapped reads. And also, there are many different normalization method in bamCoverage(RPKM, CPM, BPM, RPGC, and so on). If I compare with all the bigWig files(actually it is ChIP-seq), which one is the best normalization method?

Thank you for in advance!

[LeilyR]

Hi, I would recommend you to check the documentation for the description of different methods. However, for ChIP data you could use RPGC or RPKM.

[dahun73]

Thank you for reply :)

I usually use RPGC option too. But I'm worried about whether I used proper normalization options among different samples. When I watch different samples of bigWig, there are different library read length. I've known that it should be set by organism and library read length. Is it okay just setting by organism?

For example, I have 2 ChIP-seq samples(mouse). For the library read length, one is 75bp and the other is 150bp. I want to compare with these two samples. Then, I decide to use RPGC normalization option. In this case, is it okay using '--effectiveGenomeSize 2652783500'? This value was written in manual(GRCm38).