NAME

       sga2bed - Convert SGA format into BED format

SYNOPSIS

       sga2bed [options] [<] <SGA 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 chr_NC_gi file [default is: $HOME/db/genome]

       -l|--readlen <len>
              Set Read length <len> Unoriented SGA files are extended by +/-<len>/2

       -c|--score <score>
              Normalisation factor for BED score field (5th) [score=1]

       -n|--norm
              <normf>        Normalisation factor for BED score field (7th) [normf=1]

       -e|--extend f1:F1[,f2:F2] Set SGA optional field(s) f1(,f2,...) to BED field(s) F1,(F2,..)
              Fields  are  specified  by column numbers Accepted BED field values are 4, 5, and 7
              Except BED field 5 (score field), BED fields 4 and 7 can be used  to  set  multiple
              extension  values from SGA Fields 5 and 7 convert into numerical values whereas BED
              field 4 takes character strings as they are

       -r|--nohdr
              BED format without annotation track header lines

       -x|--expand
              Expand SGA lines into multiple BED lines

       --name <name>
              Set name for track name field [def. name=SGA-feature]

       --desc <desc>
              Set track description field [def. desc="ChIP-Seq Custom data"]

       --color <col>
              Define the track color in comma-separated RGB values [def. 100,100,100]

              Convert SGA format into BED format.

AUTHOR

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.