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Old 05-04-2012, 03:57 AM   #8
Junior Member
Location: Sweden

Join Date: Jan 2012
Posts: 8

Hello members. Thank you for your valuable advice.

I've run assemblies on my data using Trinity,Newbler,MIRA,velvet on my HP laptop which has 4GB RAM and i3 processsor. About 800k reads with both genotypes pooled together.
No, i have not tried M.truncatula, phoss.I will,thanks!
I've pooled all the reads and assembled using MIRA + CAP3.Trinity, although a really good assembler is quite bad for plant genomes.(poor annotation, poor N50 etc)
Yes it is transcriptome. Now i suppose i will map the reads back to this 'reference', quantify and continue with the analyses.

Thanks for the Abyss suggestion and paper, jujubix & sdriscoll. I will try it out.
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