processing 454 rna-seq data

[acpatel]

OK. I have rna-seq data from 3 mice. I want to align this data to the mouse reference -- either genome, which seems like overkill, or to all the known mRNAs from Acembly -- which I have in FASTA format.

The data came from 454 as FASTA (.fna) and .qual files.

I've also obtained the SFF files.

TopHat didn't seem to like the FASTQ files I generated from the FASTA and .qual files using BioPython's SeqIO functions.

There's a really big range of read lengths in this data, which also seems to make a lot of the tools (since they were engineered for Illumina GA output) unhappy.

Thoughts? Advice? I'm on a Mac Pro, but have 64-bit linux and Windows XP running via virtualization.

Thanks,
Anand