On Sun, Oct 31, 2010 at 10:19 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> On Sun, Oct 31, 2010 at 11:10 PM, Oleg Moskvin <moskvin@wisc.edu> wrote:
> > Hello list members,
> >
> > For a RNA-seq analysis, what would you suggest to use to convert
> raw-sequence-based read coverage to annotated ORF-based coverage, if the
> genome of interest is NOT supported in neither UCSC nor ENSEMBL, which means
> that creation of a TranscriptDB object in a straightforward way (I.e.
> according to the GenomicFeatures pipeline) is impossible? What would you
> recommend to import a .gff file (containing annotation of a particular
> genome, from GenBank) into R/Bioconductor to eventually generate a
> gene-centric countTable readable by packages like DESeq?
>
> Assuming I've understood your question and how you have your data
> available to you, here is one (maybe too simple) approach:
>
> I think I'd parse the GFF into a GRangesList object (each item of the
> list would be a GRanges object that stores the exon structure of your
> transcripts (or genes) (which I'm assuming is what's in your GFF
> file)).
>
> If you had your rna-seq data in its own GRanges object, you could then
> countOverlaps between your data and GRangesList-transcript info pretty
> easily, which you could use to create your countTable.
>
> Hope that helps,
> -steve
>
> ps - I think rtracklayer has some facilities to import GFF files,
> which might be helpful to you.
>
>
Right. Just import(asRangedData=FALSE) and then split() it into a
GRangesList.


> --
> 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<http://cbio.mskcc.org/%7Elianos/contact>
>
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