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Old 11-05-2009, 02:59 PM   #1
atg...tga
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Location: SF Bay Area

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Default Annotating mRNA-Seq maps/alignments

Hey all,

Bear with me as I ask a noob question, I'm completely overwhelmed by the information on analysis software that's out there and not sure what applies to what I want to do with my data.

I have a set of mRNA-Seq raw data files (as well as eland analyzed files) from an Illumina 1G GA and I've managed to figure out how to align my reads to a reference genome (using Bowtie, yeilding .map or .sam files). Now what I really want is to get reads per gene, I'm purely interested in gene expression levels, not splice variants or stuff like that.

What would be the best way to do this? Where would one obtain the annotated reference sequences (the genbank ones on NCBI seem to all be small chunks categorized per chromosome). What software do people use for this? Any help on this is much, much appreciated.

Cliff notes: have aligned mRNA-Seq data, want reads per gene, how?
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