[BioC] DESeq and transcript-wise analysis

[Elena Sorokin]

Greetings all,

After re-reading related posts in the listserv archive, I still didn't 
know the exact answer to my question, so here goes. I'd like to use 
DESeq to measure differential isoform expression. Has Simon or anybody 
else written a script that will convert aligned reads (.bam/.sam file) 
into a table of isoform counts, suitable for input to DESEq - similar to 
what Simon has done at the gene-wise level, but instead for making a 
table of counts by isoform?

I would try to do this myself, but I'm a novice at programming. Sorry if 
this has been answered elsewhere... If so, please let me know the link.

Thanks,
Elena