=============================
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
<http://khmer-protocols.readthedocs.org/>`__ for the latest released
version.

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

.. @CTB TODO: list software we are using, and publications.

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

   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`