ERANGE – Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq

E-RANGE is aPython package for doing RNA-seq and ChIP-seq (hence the “dual-use”), and is a descendant of the ChIPSeq mini peak finder (Johnson, 2007).

To use it for RNA-seq, first go through the RNA-seq README, then read the file analysisSteps.txt and take a look at the pipeline shell script

Note that E-RANGE assumes the following requirements: Python 2.5, Linux / Mac OS X (preferably with the Python Psyco compiler), and Cistematic 2.0 (all scripts with a command line genome specification rely on Cistematic!), which you can get here.

If you want to rerun our entire analysis starting with either the raw data (eland files) or the bed files, you will need the following files:

Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (7), 621-28. [abstract]