Shift BED/GFF

Shift coordinate intervals up/downstream.

Related to the Bedtools shift function.

Input format (BED or GFF)

Use the radio buttons in the GUI or the --gff flag in the CLI to specify which format the to parse the provided input as (BED-format or GFF-format).

Shift options

• Directional shift (bp) - An upstream shift is indicated with a positive integer while a downstream shift is indicated with a negative integer.

• Use stranded info - By default this upstream and downstream shift is set with respect to the coordinate strand but can be forced to shift according to the genomic reference when this box is unchecked.

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/gff suffix.

Output GZip

Toggling this allows the user to write output to a compressed file format using a general compression (gzip) which has the added advantage of speeding up the execution time by shrinking the I/O load (esp for large output). The .gz extension will be appended as appropriate.

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)