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tboothby 12-22-2011 09:21 AM

Annotating reference followed by mapping?
Hi all,
I am trying to map RNAseq data generated from 3 different time points during my organisms development to a reference transcriptome.

I have assembled the reference transcriptome de novo, and am wondering if there is a way (and if so how) to annotate that reference, such that when I map my reads to it (TOPHAT/BOWTIE) I can get annotations of my mapped reads?

*edit* by annotations I basically mean blast results (E.g. what the transcript is)

Does that make sense? I assume there is a way to do this, but I don't know how.


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