Non-model organisms and RNAseq

With non-model systems, where there is neither a good genome nor a lot of mRNAseq data, you have to build your own transcriptome from scratch – so-called “de novo transcriptome assembly”. There are a few programs to do this - most notably Trinity and Oases - and we have found little difference.

The main problem you’ll run into with non-model mRNAseq is that the output is fairly noisy with respect to splice variants. Our experience has been that many of these splice variants are probably “real” – in the sense of actually present – but may be biological “noise”, in the sense that they are not actually functional (See this excellent paper by Pickrell and Pritchard making the case). Regardless, there’s little that you can do about this, although we will talk about it a bit on the second day.

The overall process


This gives you an assembled transcriptome, consisting of many transcripts and transcript families.

At this point you can do one or more of the following:

Next: Getting started with Amazon EC2

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