sga2bed - Convert SGA format into BED format
sga2bed [options] [<] <SGA
file|stdin>
- - 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.
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.