Shift BED/GFF
Shift coordinate intervals up/downstream.
Related to the Bedtools shift function.
Output format
For each input BED/GFF file, a new BED/GFF file is created with the original filename that has been stripped of its original extension and replaced with the *_shift<+or-><sizeofexpansion>bp.bed suffix. If the "Output GZIP" checkbox is slected, the .gz extension will also be appended.
Command Line Interface
Usage:
java -jar ScriptManager.jar coordinate-manipulation shift-coord [-huVz] [--gff]
[-o=<outputFilepath>] [-t=<shift>] <input>
Positional Input
This tool takes a single BED file for input.
Output Options
| Option | Description |
|---|---|
-o, --output=<outputFilepath> | specify output filepath (default input filename with _shiftXXXbp.bed/gff) |
-z, --gzip | gzip output (default=false) |
--gff | input is GFF format (default=BED format) |
Shift Options
| Option | Description |
|---|---|
-t, --shift=<shift> | shift distance in bp, upstream < 0 and downstream > 0 (default=0) |
-u, --unstranded | don't force strandedness (default=forced) |