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.mskc="" c.org="" %7elianos="" contact=""> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]