extend_bed.pl - Extends bed entries strand specific one- or two-sided.
extend_bed.pl [-g FILE] [-b FILE] [-o FILE] [-e Interger] [-l Interger] [-r Interger] [-u Interger] [-d Interger] [options]
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.
File containing chromosome sizes
BED file for extension
Output file name
Extension to total length from both sides
Extension to total length from 5' end
Extension to total length from 3' end
Upstream only extension to total length from 5' end. Can be combined with -d to get upstream extension, plus extension into original coordinate span
Downstream only extension to total length from 3' end. Can be combined with -l to get downstream extension, plus extension into original coordinate span
Print short help
Prints the manual page and exits
Joerg Fallmann <joerg.fallmann@univie.ac.at>
To install Bio::ViennaNGS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::ViennaNGS
CPAN shell
perl -MCPAN -e shell install Bio::ViennaNGS
For more information on module installation, please visit the detailed CPAN module installation guide.