Refining Transcriptome Assembly

crader · 09-18-2011, 06:05 AM

Hi,

I'm doing some transcriptomics on a non-model (an earthworm) and am having issues with my assembly.

I've got HiSeq RNAseq data from pooled samples (around 20-25 monophyletic) individuals for each of 3 exposures. I've assembled the transcriptome of a single exposure group using Velvet and Oases, but I've got a massive haul, with an N50 of 82,694 >= 1465 bp.

I anticipate that vast amount of variation within my sample will mean that theres an awful lot of very similar sequences in my data- What software is out there to help me achieve a consensus transcriptome?

I really would appreciate any pointers,

Craig

P.S. There is a draft reference genome for this species, but its of a genetically distinct (14% according to mitochondrial COII markers and AFLP) alternative lineage.

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09-18-2011, 06:05 AM	#1
crader Member Location: Cardiff, UK Join Date: Sep 2010 Posts: 12	Refining Transcriptome Assembly Hi, I'm doing some transcriptomics on a non-model (an earthworm) and am having issues with my assembly. I've got HiSeq RNAseq data from pooled samples (around 20-25 monophyletic) individuals for each of 3 exposures. I've assembled the transcriptome of a single exposure group using Velvet and Oases, but I've got a massive haul, with an N50 of 82,694 >= 1465 bp. I anticipate that vast amount of variation within my sample will mean that theres an awful lot of very similar sequences in my data- What software is out there to help me achieve a consensus transcriptome? I really would appreciate any pointers, Craig P.S. There is a draft reference genome for this species, but its of a genetically distinct (14% according to mitochondrial COII markers and AFLP) alternative lineage.