NAME

extend_bed.pl - Extends bed entries strand specific one- or two-sided.

SYNOPSIS

extend_bed.pl [-g FILE] [-b FILE] [-o FILE] [-e Interger] [-l Interger] [-r Interger] [-u Interger] [-d Interger] [options]

DESCRIPTION

This program extends Bed files to a total length of at least -e, -r or -l nucleotides, or at least to begin or end of the corresponding chromosome. Furthermore 3' or 5' end extension is possible, where only up- or downstream regions can be retrieved, or combinations of the latter with extension into the original coordinate span.

OPTIONS

-g

File containing chromosome sizes

-b

BED file for extension

-o

Output file name

-e

Extension to total length from both sides

-l

Extension to total length from 5' end

-r

Extension to total length from 3' end

-u

Upstream only extension to total length from 5' end. Can be combined with -d to get upstream extension, plus extension into original coordinate span

-d

Downstream only extension to total length from 3' end. Can be combined with -l to get downstream extension, plus extension into original coordinate span

--help -h

Print short help

--man

Prints the manual page and exits

AUTHOR

Joerg Fallmann <joerg.fallmann@univie.ac.at>