Question: normalization of ChIP-seq data
0
gravatar for Bogdan
12 months ago by
Bogdan580
Palo Alto, CA, USA
Bogdan580 wrote:

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 • 204 views
ADD COMMENTlink written 12 months ago by Bogdan580

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 REPLYlink written 12 months ago by Nicolas Servant260

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 REPLYlink written 12 months ago by Bogdan580

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

ADD REPLYlink written 12 months ago by nicolas.descostes20
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