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Old 07-27-2009, 09:55 AM   #1
pfranchini
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Location: Cape Town

Join Date: May 2009
Posts: 19
Default RPKM and TopHat

Hi,
I recently collected a lot of Solexa transcriptome data about different groups of sample of abalone species and I would like to calculate gene expression through RPKM measure. I am working on a non-model organism so I donít have a reference genome. I had temporary access to the CLC workbench software and I tested its mRNA-Seq option using as reference file the same contigs file built de novo by Velvet. Now I would like to do replicate this approach with other free programs. I saw that TopHat gives the RPKM measure but only if a gff3 file is supplied. Is there a way to manipulate my contigs file (a simple fasta file) and format it like a gff3 file? My idea was to consider each sequence in the list of my contigs as a "gene" for the gff3 file, assuming the absence of introns in them.
Thanks,

P
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