============================= The Eel Pond mRNAseq Protocol ============================= :author: C. 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 <../index.html>`__ for citation information, and `the khmer-protocols site `__ for the latest released version. 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: .. toctree:: :maxdepth: 1 0-download-and-save 1-quality 2-diginorm 3-big-assembly installing-blastkit 5-building-transcript-families 6-annotating-transcript-families 7-expression-analysis 8-differential-expression Reference material ------------------ :doc:`../docs/command-line` :doc:`../amazon/index`