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

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.

 

 

 

 

 

Skip to end of metadata
Go to start of metadata

Peak Ranger

Peakranger_wig_1.18 generates variable step format wiggle file.

 

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 "Data 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)

  • PeakRanger_wig_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