Ali Mortazavi, Brian Williams, Kenneth McCue, Lorian Schaeffer, Barbara Wold
This page holds the underlying data and code for the analysis of the paper above, which has been published in Nature Methods in 2008. While the paper focuses on mouse tissues, we have since used the same code in C elegans and human cell lines with great success.
ERANGE is our Python package for doing RNA-seq and ChIP-seq (hence the "dual-use"), and is a descendant of the ChIPSeq mini peak finder (Johnson, 2007). In particular, the RNAseq analysis uses some of the very same code to access Cistematic. Version 2.0 is the first released in the wild and is "Bed"-centric. In particular, it is not optimized for speed!
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 runStandardAnalysis.sh.
Note that ERANGE 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:
Briefly, each tissue has two replicates, the second of which was done with spike-ins, as desribed in the paper. For each replicate we provide: