Align BED to Reference

Align BED peaks to Reference BED file creating CDT files for heatmap generation

File Inputs (BED)

This script expects both a Peak BED file input and a Reference BED file input.

Command Line Interface

Usage:

java -jar ScriptManager.jar peak-analysis peak-align-ref [-hV] [-o=<output>]
<peakBED> <refBED>

Input	Description
<peakBED>	The BED peak file
<refBED>	The BED reference file

Output Options

Option	Description
-o, --output=<output>	specify output file (default=<peakBED>_<refBED>_Output.cdt)