Rat lung transcriptome

Question

[pel]

We ran RNA-seq for rat lung tissue, and need to build an index for tophat2 (bowtie) that reads this index (fasta). I searched for downloads of rat transcriptomes at UCSC and noticed most of their data is genomic.

Has anyone produced a rat lung transcriptome fasta?

[Ram]

You seem to be looking for a reference transcriptome, which is a genome sequence with gene annotations. If that is true, I think you should mention the exact species you're looking for. And unless I'm mistaken, you should be able to get genome FASTA as well as feature GFF/GTF files from UCSC.

EDIT: This might be of use: http://ccb.jhu.edu/software/tophat/igenomes.shtml

[pel]

thx - used the table browser at UCSC, downloaded the fasta mRNA sequences for the rat transcriptome, then created an index using bowtie_build.