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Old 07-05-2010, 10:10 PM   #1
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Location: Hobart, Australia

Join Date: May 2009
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Default Velvet/Oases transcript expression level?

I am in the process of de novo transcriptome assembly from a non-model eukaryote. I have 17 million 65 bp, paired-end reads that I have assembled with Velvet and then Oases. This gives nice results in that I am getting full-length contigs that appear reasonable when compared to orthologues in related model eukaryotes. However, I am really after relative transcript expression levels. Does anyone know if there as a way that I can get information on that from this software combination? is offline   Reply With Quote
Old 08-10-2010, 03:03 AM   #2
Location: Exeter, UK

Join Date: Jan 2009
Posts: 17

Hi Simon,

I'm not by any means an expert on this, but you probably have two options:

1. Convert the kmer coverage in the stats.txt file to base-coverage and use that as a proxy for expression level

2. Align the reads to the assembled transcripts using something like Bowtie and then extract the coverage of each transcript using SAMTools

Hope that helps!
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Old 08-11-2010, 05:33 AM   #3
Location: Michigan

Join Date: Jul 2009
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Default Velvet question

How can one extract all of the reads that were used in the assembly, in order to do the re-mapping step you described?
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Old 08-11-2010, 09:47 AM   #4
Location: Exeter, UK

Join Date: Jan 2009
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Under the contrib/extractContigReads directory in Velvet you'll find a script to do this
konrad98 is offline   Reply With Quote

expresison, oases, quantification, rna seq, velvet

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