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.