[BioC] Illumina DGE => sRNA detection pipeline

Steve Lianoglou mailinglist.honeypot at gmail.com
Thu Oct 14 00:26:11 CEST 2010

Hi Oleg,

On Wed, Oct 13, 2010 at 5:39 PM, Oleg Moskvin <moskvin at wisc.edu> wrote:
> Hello list members,
> I usually work in R environment for most of my projects. I am interested in using R/Bioconductor to detect small RNA species in Illumina DGE data. After reviewing available Bioconductor packages, I have an impression that there is no establisted pipeline to do that (is that true?). I'd like to hear from the list members who successfully used Bioconductor resources for this purpose.

When you're talking about DGE, are you talking about the SAGE-like tag
profiling protocol from Illumina?

If so, then I'm pretty sure there isn't an established pipeline. I've
been developing some packages that deal with this type of data to take
it from raw reads -> stripped adapters -> alignment -> annotated tags.
I'd like to add it to the bioconductor-package universe in due time,
but it's not really ready for public consumption.

I'm a bit surprised that you're using DGE (the type I'm thinking of)
to detect small RNAs, though, so maybe we're not talking about the
same thing (?).

Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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