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Old 03-04-2011, 04:43 AM   #6
Location: Germany

Join Date: May 2008
Posts: 79

Originally Posted by Vickenstein View Post
[...] Now I am about to sequence the same transcriptome using Illumina 75+ bp platfrom. [...]
I am contemplating the assembly software that I should be using.
I use the current development version of MIRA (V3.2.1.8) and just went through a RNASeq denovo 100bp with 22m reads.

Originally Posted by Vickenstein View Post
I really like newber's isoform prediction, and am not sure if it possible to merge both sets of raws reads together in an good assembly.
It is. I regularly use MIRA for genome de-novo with 454 and Illumina (ranging from 36 to 100mers). Should also work with mixed transcriptome.

Originally Posted by Vickenstein View Post
I haven't seen any software out that are able to utilize a transcriptome reference for assembling new reads
MIRA. No problem if your reference is a transcriptome, but stay away from trying to map RNASeq to a genome, that will fail miserably at intron/exon boundaries.


Disclaimer 1: I'm the author of MIRA, your mileage may vary (but then I'd like to hear about it)
Disclaimer 2: for data sets with more than 40m reads you probably want to wait for a next version.
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