Peak Ranger is a fast, optimized ChIP-seq tool developed in partnership with the modENCODE project.
- To use PeakRanger, upload your data in BED, BOWTIE, SAM, or BAM format.
- Resources: documentation
Community Data > iplantcollaborative > example_data > peakranger
- 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.
- Several files are emitted by PeakRanger. Results from the test case are as follows: