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).
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:
- ERANGE2.tgz (the code)
- mm9splices_spikes.tgz (the files for building the exapnded genomes and remapping splices)
- RNAFAR.tgz (the consolidated RNAFAR analysis, includes repeat library from UCSC – large!)
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]