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.

sga2bed 1.5.5                                      March 2020                                         SGA2BED(1)