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Old 01-12-2012, 04:33 PM   #6
RogerH
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Location: Townsville, Australia

Join Date: Dec 2011
Posts: 6
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Thanks, this is really helpful.

I'm mainly interested to find a handful of housekeeping genes and another handful of genes of interest to design qPCR primers for unsequenced species, but not a complete transcriptome at this stage.

I did manage to find some sequences that did match published sequences of my key enzyme, but there were also some weird results.

As I said, I'm a bit behind with my PhD (who isn't) and I'm hard pressed for time this year. So I think I will just go ahead and try to find my enzymes with the assembly I have, but also assemble a better transcriptome at the side.

240k transcripts in 2 weeks is fairly ambitious based on my experience. I annotated 5 different species in parallel, and the one with 80k transcripts took over a month. But maybe I was doing something wrong. I might look into a local blast to speed up things for my annotation of the untrimmed data.
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