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index.txt
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index.txt
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=============================
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.
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`