The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Peak Ranger

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

Quick Start

  • To use PeakRanger, upload your data in BED, BOWTIE, SAM, or 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.sam  as the "Sample (IP) alignment file:" and use AP2_CNTL.sam  as the "Control (WCE/no Ab) alignment file". Indicate that these are SAM format files using the drop-down box

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)

  • Several files are emitted by PeakRanger. Results from the test case are as follows:
    AP2_CNTL.sam.wig
    AP2_REP2.sam.wig
    peakranger_details
    peakranger_region.bed
    peakranger_summit.bed

Tool Source for App