Peak Ranger

Peak Ranger is a fast, optimized ChIP-seq tool developed in partnership with the modENCODE project.

Peak Ranger_wigpe_1.18 generates a bedGraph format wiggle file and supports spliced alignments and thus only supports bam files.

Quick Start

• To use PeakRanger_wigpe_1.18, upload your data in BAM format.
• Resources: documentation

Test Data

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data >  peakranger

Input File(s)

• Use AP2_REP2.bam  as the "Data file:"

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

• Use these parameters within the DE app interface:
  • Pad read coverage profiles - true
  • Leave all other parameters their default values.

Output File(s)

• PeakRanger_wigpe_1.18 produces one output file when run with the example data and parameters. Results from the test case are as follows:
  peakranger.wig

Tool Source for App

• http://ranger.sourceforge.net/