On Wed, Oct 13, 2010 at 5:39 PM, Oleg Moskvin <moskvin@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.
>
>
Hi, Oleg.  Not sure what you mean by Illumina DGE data, but the first place
to start is to determine if the protocol used in sequencing even captures
small RNA species.  If so, does the alignment method capture them if they
are present in the sequencing data?  If the answer to both is true, then you
could potentially use the same counting infrastructures as are used for
RNA-seq or for ChIP-seq (peak-finding).  As with many sequencing
applications, though, the approach will depend on the details of the
experiment.  Perhaps some more detail would be helpful.

Sean

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