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.

bed2sga 1.5.5                                      March 2020                                         BED2SGA(1)