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.