Normalize ChIP-seq samples with different signal-to-noise ratio
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@1eb02517
Last seen 3 months ago
Spain

Hello everyone! I have a question about a histone marks ChIP-seq experiment. When I normalized my samples with RPKM or TMM, I realized WT condition has a higher signal everywhere (background and peaks detected by macs2). So although the signal-to-noise ratio is lower than the mutant condition, the signal in the peaks is higher, even in regions I had checked by RT-qPCR before sequencing. I was wondering If there is a way to normalize the samples according to the background of each one, or any normalization method to solve this problem.

csaw edger tmm chipseq • 240 views
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Cross-posted to Biostars https://www.biostars.org/p/9515077/

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Rory Stark ★ 4.4k
@rory-stark-5741
Last seen 12 days ago
CRUK, Cambridge, UK

The csaw user guide has a detailed discussion of normalizing ChIP-seq samples, as does the DiffBind vignette. Those would be good places to start.