[BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION

Steve Lianoglou mailinglist.honeypot at gmail.com
Thu Aug 16 19:25:36 CEST 2012


On Thu, Aug 16, 2012 at 1:17 PM, Richard Friedman
<friedman at cancercenter.columbia.edu> wrote:
>         I would like then to ask a broader question - one that I was
> going to ask after I completed the vignette:
> Is it possible to obtain annotation for RNASeq data analogous
> to the kind obtained for microarrays?
> To be specific, when I analyze affymetrix microarrays I get, for
> each probeset the Entrez gene symbol and a description of the gene
> which could be several words long, as well as gene ontology categories
> and pathways. I can output this information as an Excel spreadsheet.
> When I work through  the drosophila vignette with transcriptCounts or
> geneCounts I got accession numbers (e.g.,"FBtr0005009") but no gene
> symbols etc.
> Do you have any suggestions as to how to get Entrez Gene Symbols,
> descriptions, etc, for RNASeq output with easy RNASeq?

Perhaps I'm missing something, but given accession numbers (or other
gene identifiers), it should be pretty straightforward to jimmy up
something using the org.*.eg.db packages, no?

I suspect you won't get gene descriptions there -- but if I were a
gambling man, I would bet you can probably get that last piece of the
puzzle from biomaRt.


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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