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.