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BED2SGA(1) User Commands BED2SGA(1)

NAME

bed2sga - Convert BED format into SGA format.

SYNOPSIS

bed2sga [options] [-s <s_assembly (e.g. hg19)>] [<] <BED 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 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 -u are ignored]
Convert BED format into SGA format.

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
March 2020 bed2sga 1.5.5