[eppi]

Hi AmyEllison,

we got 'only' >1,5 million contigs....so I dropped the ball and thought something was wrong. I must say that I mapped only 1 of the sample back to the assembly, so maybe it is a sample specific issue. Therefore, I am inclined to think that it could be from pooling samples. (by the way the GB of the machine were about 244). Thanks!

[crusoe]

It is our (GED Lab, the home of the khmer project) experience that diginorming prior to running Trinity works as well and is faster than Trinity's built-in implementation.

Our mRNASeq protocol can guide one through the entire process: http://khmer-protocols.readthedocs.o...seq/index.html

We have also greatly improved the installation procedure: http://khmer.readthedocs.org/en/latest/install.html

Cheers,