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

[Richard Friedman]

Steve,

	Thanks. I use annaffy for microarrays and was hoping for an
already-worked-out protocol. I will however look into the package
you recommend if no more explicit protocol is available.

Best wishes,
Rich

On Aug 16, 2012, at 1:25 PM, Steve Lianoglou wrote:

> Hi,
> 
> On Thu, Aug 16, 2012 at 1:17 PM, Richard Friedman
> <friedman at cancercenter.columbia.edu> wrote:
> [snip]
>>        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?
> [/snip]
> 
> 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.
> 
> HTH,
> -steve
> 
> -- 
> 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