Can I get this data in a form that can be processed by Cufflinks using
the tools available on Galaxy or not? So far I haven't been able to
figure this out.
You probably know that Cufflinks requires SAM files to be sorted by chromosome name and position. We're working to add the samtools sort to Galaxy. In the meantime, you can sort a SAM file using this workflow: http://main.g2.bx.psu.edu/u/jeremy/w/sort-sam-file-for-cufflinks
(Click 'import' to copy it to your workspace.)
I assume that Cufflinks is the only (best?) way to look at transcript
abundance on Galaxy?
Currently,Cufflinks is the only way to look at transcript abundance.