On Mon, Mar 1, 2010 at 4:46 PM, Raphael Gottardo <raphaelgottardo@mac.com>wrote:

> Hi Michael (and others),
>
> I would certainly second that. You guys have develop great tools for low
> level analysis of next gen data, but higher level analysis are still lagging
> behind. Though, this is rather normal as the higher level stuff needs the
> lower level infrastructure.
>
> My group has been working on several aspects of chip-seq analysis and to
> some extend gene regulation.
> As noted in one of the email this morning, we are about to submit our PICS
> software based on a version of this paper http://arxiv.org/abs/0903.3206,
> which we hope will be published in Biometrics in the near future. For our
> package we have used some of the infrastructure available in the chip-seq
> package, and IRanges.
>
> One the problem we have faced is data input. In chipseq, one does not need
> sequence reads. However, when you use ShortReads you automatically get the
> sequence reads which takes a lot of memory. For some highly sequenced data
> we have, it has been somewhat of a bottleneck.
> So it would be nice to be able to only read the chr/start/strand
> information. As pointed out by Wolfgang, rsamtools might be the solution, so
> we will have to see how we can use rsamtools and the classes defined there
> for chip-seq. This being said we still have a lot of files from non MAQ
> aligners.
> I think Arnaud Droit, who is in my group, has sent an email about this
> issue already.
>
> Besides PICS that will be submitted this week, we have already released a
> package for motif analyses, rGADEM, which can work on standard Biostrings
> objects. rGADEM is relatively fast and well adapted for ChIP-seq enriched
> regions. We also have another package, MotIV for motif validation and
> identification based which is based on STAMP (with many improved
> functionalities). MotIV is under review I believe and should be available
> soon.
>
> Anyway, so very soon we will have a complete pipeline from shortread ->
> enriched regions (PICS) -> motifs (rGADEM) -> validated motifs and motif
> occurrences (MotIV) -> other BioC packages (e.g. GenomicsFeatures, etc).
>
>
This all sounds exciting. I want to clarify though that I am not proposing
Bioconductor adopting a particular pipeline/methods, rather that we provide
an extra layer of infrastructure to make developing pipelines easier.


> So at least this will be a start. Of course we are open to
> suggestions/requests, etc. If any of you guys want more details feel free to
> drop us an email.
>
> Cheers,
>
> Raphael
>
> On 2010-03-01, at 10:08 AM, Michael Lawrence wrote:
>
> > Hey guys,
> >
> > I'm wondering if anyone has given any thought to some sort of generic
> > framework for chipseq analysis in Bioconductor, based on the IRanges,
> > Biostrings, etc infrastructure. chipseq has some nice utilities; could it
> be
> > transformed into some sort of generic chipseq pipeline? Something like
> how
> > the 'affy' package (I think?) allows other packages to provide
> alternative
> > implementations for particular stages. Just having a clean, refined,
> > approximately complete set of chipseq-focused utilities would be nice.
> > Presumably chipseq could fill that role? I think we now have a good idea
> of
> > the basic steps in chipseq analysis, so it's probably time for such a
> > package to emerge.
> >
> > Comments?
> >
> > Michael
> >
> >       [[alternative HTML version deleted]]
> >
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>
>

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