Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
RPKM and multiple reads, tophat and cufflinks mgogol Bioinformatics 6 09-03-2012 02:46 PM
tophat, not producing rpkm values with -G option warrenemmett Bioinformatics 6 06-02-2010 07:31 AM
tophat/cufflinks bam vs. RPKM mgogol Bioinformatics 5 04-26-2010 09:58 AM
RPKM as calculated by TopHat rpm16 Bioinformatics 1 10-21-2009 08:27 AM
Tophat : percentage of reads contributing to RPKM values sdriscoll Bioinformatics 19 10-16-2009 04:01 PM

Thread Tools
Old 07-27-2009, 08:55 AM   #1
Location: Cape Town

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

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.

pfranchini is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 11:47 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO