[BioC] DESeq and transcript-wise analysis
Elena Sorokin
sorokin at wisc.edu
Thu Feb 9 00:26:19 CET 2012
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
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