[Bioc-sig-seq] ChIP-seq analysis in normalization/peak calling between sample and control

[Raphael Gottardo]

Hello Charlie,

The PICS software is currently under revision for BioC and should be available very soon. If you want an advanced copy we could send you one. Just contact me offline. The PICS paper has been accepted to Biometrics, I will try to post an updated version on my website tomorrow.

We have tried to make PICS as simple as possible, so it should fit your needs. We also have two other packages to complement PICS that are already available from the devel version of BioC (rGADEM and MotIV). These two will work on the enriched sequences and will perform motif analysis and post-processing. 

Please let me know if you have any questions.

Raphael

On 2010-03-26, at 6:02 PM, Chen-Yi Chen wrote:

> Hi all,
> After going through all the ChIP-seq pipeline in ht-seq, I finally come down to normalization/peak calling. Interestingly, ht-seq seems to not have a standard normalization and peak calling algorithm between sample and control. I've read through the previous threads about "peaks calling," and people suggest all different things.
> So I've tried the following packages:
> chipseq -> using the cutoff as island/peaks calling, and there is nothing about normalization technique. From my understanding, I thought we need a normalized data from sample and control in order to do this, and I certainly don't know how to normalize them in ht-seq.
> SPP -> didn't work, it returned a NaN out of range error when doing the enrichment (peak calling) calculation.
> CSAR -> didn't seem to be available in installation through biocLite, but I downloaded and installed it manually. It didn't seem to work well with ShortRead. (at least I have no idea how to do it), and again, wig file output didn't visualize on UCSC genome browser.
> ChIPseqR -> I didn't go in to it that much, but it seemed to be the "simulating package"
> ChIPsim -> similar story as ChIPseqR
> PICS -> I visited their website and they mentioned it should be available through bioconductor website, but I didn't see any PICS packages on bioconductor website.
> 
> Is there a standard (or simple) normalization technique/peak calling package in ht-seq that we can use?
> I am not a statistician, so any suggestions on this normalization/peak calling would really help our analysis.
> 
> Thanks a bunch!
> 
> -Charlie-
> 
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