I'm moving your email to the galaxy-user mailing list because it concerns
galaxy usage; also, there's a substantial community of users doing RNA-seq that
may be able to offer suggestions to help you out.
To your issue:
> I used Galaxy (Bowtie) to successfully map 15 million Illumina reads trimmed
> to 65bp. When I applied Cufflinks to the BAM data no transcripts were
> reported even though it ran OK. It is possible that very little mapped to
> known exons in this data set. Does Cufflinks only report data for known
> transcripts? I thought it was designed to work without a reference
> annotation. How does it decide what qualifies as a transcript? Any ideas
> why I got such a result?
Your problems are likely at least partially due to using Bowtie instead of
Tophat. Tophat is the standard way to map reads so that Cufflinks can assemble
transcripts. Cufflinks assembles transcript--de novo or reference-guided--based
on the mapped reads, but mapped reads must include spliced reads, which are
generated by Tophat but not Bowtie.
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