If anyone is interested it seems that rSeq (http://biogibbs.stanford.edu/~jiangh/rseq/) can do exactly this. The program calculated RPKM using a reference transcriptome rather than a genome.
-John
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ERANGE: map to transcriptome
Hi All,
I am attempting to get ERANGE up and running but have a few questions before I commit more time to it.
Specifically, after reading the documentation I've noticed genes are predicted from the genome file. Rather than running a gene prediction algorithm for an already annotated genome, I was wondering if this step could be bypassed by using a reference transcriptome instead.
Are there any disadvantages of doing this? One issue that I see is that the RPKM calculations would be off (variables C and N).
Thanks,
John
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