RNAseq transcriptome

[biofreak]

hi All,
I want to align my RNAseq data (reads) to the "transcriptome" and not the entire reference genome. Where can I download this data form?
Can someone please help?

[kmcarr]

What species are you working in? And why do you want to align to the transcriptome instead of the genome?

[biofreak]

I am working with human and mouse data. I thought aligning it to reference transcriptome would be considerably faster?

[Artur Jaroszewicz]

Does anybody know where to download one? I can create one, but it would take a while, I think. Biofreak, have you found one?
Best,
Artur

[IsmailM]

human transcriptome

check here for human mrna

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/

[yueluo]

You could also try Ensembl.

http://www.ensembl.org/index.html

[Wallysb01]

The current tophat pipeline creates a transcriptome from your gtf/gff file to map to first, then goes on to mapping the unmapped reads to the rest of the genome. If you prebuild the transcriptome index and reuse it, it certainly helps with the speed.