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.