NAME¶

bed2sga - Convert BED format into SGA format.

SYNOPSIS¶

bed2sga [options] [-s <s_assembly (e.g. hg19)>] [<] <BED file|stdin>

DESCRIPTION¶

- version 1.5.5 where options are:

-d|--debug

Produce Debug information

-h|--help

Show this Help text

-i|--db <path>

Use <path> to locate the assembly-specific chr_NC_gi file [default is: $HOME/db/genome]

-f|--feature <ft>

Set Feature name <ft>

-s|--species <spec>

Assembly <spec> (i.e hg19)

-c|--center

Generate a Centered SGA file

-u|--unoriented

Generate an unoriented SGA file

-r|--regional

Generate a 2-line[+/-] SGA file representing BED regions (e.g. RepeatMasker regions)

-e|--extend <f1,f2,...>

Produce an extended SGA file with additional fields specified by a comma-separated list of BED column numbers (from 1 to n)

--useScore

Use the BED 'score' field (#5) to set the SGA 'count' field

--useSigVal

Use the BED 'Signal Value' field (#7) to set the SGA 'count' field [This option is only valid for ENCODE narrowPeak]

--narrowPeak

Use this option for ENCODE narrowPeak format [Options --useScore, -c, and -u are ignored]

Convert BED format into SGA format.

AUTHOR¶

This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.