bed2sga - Convert BED format into SGA format.
bed2sga [options] [-s <s_assembly (e.g.
hg19)>] [<] <BED file|stdin>
- - 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.
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.