normalization of ChIP-seq data

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Bogdan ▴ 670

@bogdan-2367

Last seen 6 months 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 • 845 views

ADD COMMENT • link 5.5 years ago Bogdan ▴ 670

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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

ADD REPLY • link 5.5 years ago Nicolas Servant ▴ 260

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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 !

ADD REPLY • link 5.5 years ago Bogdan ▴ 670

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

ADD REPLY • link 5.5 years ago nicolas.descostes ▴ 20

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