The Eel Pond mRNAseq Protocol

  1. Titus Brown, Camille Scott, and Leigh Sheneman.

This is a lightweight protocol for assembling up to a few hundred million mRNAseq reads, annotating the resulting assembly, and doing differential expression with RSEM. It is part of khmer-protocols; see the main page for this version for citation information, and the khmer-protocols site for the latest released version.

This protocol assumes that you have short-insert paired-end Illumina reads.

Special thanks to Dr. Joshua Rosenthal for his help in developing this, and to Dr. Leslie Babonis for her feedback on various problems!

The tutorial:

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github.
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