Thank you all for your reply.
I also thought of using ChIP-seq tools, but was not sure they will work
well since they all were designed for genome-wide rather than
transcriptome-wide analysis.
Mali
On Tue, Aug 23, 2011 at 2:34 AM, Mercier Eloi <emercier@chibi.ubc.ca> wrote:

> **
> Hi,
>
> I just want to mention that we developed a pipeline for ChIP-seq analysis
> including :
> *PICS for peak calling,
> *rGADEM for *de novo* motif finding,
> *and MotIV for PWMs manipulation and identification.
> I think that it can be easily tweaked for CLiP-seq as mentioned by Martin.
> These three packages are currently available in Bioconductor.
>
> Eloi
>
>
> On 11-08-20 07:14 PM, Martin Morgan wrote:
>
> On 08/18/2011 06:02 AM, mali salmon wrote:
>
> Hi All
> Does anyone know of a package to help with the analysis of RIP-seq and/or
> CLIP-seq data?
>
>
> Hi Mali -- No direct experience on my part and I don't think there's a
> CLIP-seq package per se, but it sounds like the basic tools of ChIP-seq --
> ShortReadQ or perhaps DNAStringSet from Biostrings and the IRanges
> infrastructure for pre-processing, alignment using a third-party tool (or
> perhaps Biostrings::matchPDict), GappedAlignments for representing aligned
> reads, coverage and slice for identifying enriched regions, maybe GRanges,
> GenomicFeatures, ChIPpeakAnno for annotation -- would be useful here. There
> are some approaches to peak calling in the chipseq package, including its
> vignette. I'm not sure about general-purpose MEME finding within
> Bioconductor, though there are position weight matricies in Biostrings. Hope
> that's helpful without being to vague or misleading.
>
> Martin
>
>
> Thanks
> Mali
>
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>
>
>
>
> --
> Eloi Mercier
> Bioinformatics PhD Student, UBC
> Paul Pavlidis Lab
> 2185 East Mall
> University of British Columbia
> Vancouver BC V6T1Z4
>
>

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