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Old 10-26-2009, 02:22 PM   #1
jgibbons1
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Location: Worcester, MA

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Default 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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Old 10-27-2009, 07:48 AM   #2
jgibbons1
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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, expression, illumina, rna-seq, solexa

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