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David Reiss edited this page Jun 3, 2015 · 15 revisions

The EGRIN2 pipeline

including running multiple cMonkey2 runs and postprocessing the cMonkey2 results is as follows:

  1. Run ensemble of cMonkey2 runs
  2. FIMO
  3. Coding fractions
  4. TOMTOM
  5. Motif clustering
  6. Corem discovery
  7. TBD: Inferelator!

A summary of running the EGRIN 2.0 postprocessing steps (1-6) is in a Google doc for now.

The wiki describing initial "building" of the cMonkey2 ensemble for submission to an SGE cluster and subsequent "assembly" and "querying" of ensemble is available here

Note that there are also ipython notebook ("live") versions of these wiki documents, which can be accessed here

Code is now at https://github.com/baliga-lab/egrin2-tools

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