bed2sga1
Convert bed format into sga format.
Usage
bed2sga {[options]
[-s
<s_assembly
(e.g.
hg19)>]
[<]
<BED
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 assembly-specific chr_NC_gi file [default is: $HOME/db/genome]
-f|--feature <ft>-
Set Feature name <ft>
-s|--species <spec>-
Assembly <spec> (i.e hg19)
-c|--center-
Generate a Centered SGA file
-u|--unoriented-
Generate an unoriented SGA file
-r|--regional-
Generate a 2-line[+/-] SGA file representing BED regions (e.g. RepeatMasker regions)
-e|--extend <f1,f2,...>-
Produce an extended SGA file with additional fields specified by a comma-separated list of BED column numbers (from 1 to n)
-
--useScore -
Use the BED 'score' field (#5) to set the SGA 'count' field
-
--useSigVal -
Use the BED 'Signal Value' field (#7) to set the SGA 'count' field [This option is only valid for ENCODE narrowPeak]
-
--narrowPeak -
Use this option for ENCODE narrowPeak format [Options
--useScore,-c, and-uare ignored]
-
Convert BED format into SGA format.
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).