normalization of ChIP-seq data
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Bogdan ▴ 620
@bogdan-2367
Last seen 16 days ago
Palo Alto, CA, USA

Dear all,

please may I ask about your suggestions regarding the packages/methods that are available in R/BioC that I could use for ChIP-seq normalization (shall I compare two ChIP-seq datasets : before_treatment, and after_treatment). thanks a lot !

-- bogdan

normalization chip-seq • 342 views
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Hi Bogdan,

I would suggest to read the vignette of the csaw package if you plan to work on genomic bins.

You can also look at the DiffBind package. For differential analysis at peak or gene level, from my experience, methods like edgeR works fine.

Best
 

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Thank you Nicolas. Yes, we have used before edgeR for normalization at the level of promoter/TSS area, and it is great to have your suggestions on csaw and DiffBind.  Thanks !

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you can also have a look at chipseqspike if you used spike-in controls

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