sga2bed1
Convert sga format into bed format
Usage
sga2bed {[options]
[<]
<SGA
file | stdin>}
Overview
-
- 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
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--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]
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Convert SGA format into BED format.