DOKK / manpages / debian 11 / chip-seq / bed2sga.1.en
BED2SGA(1) User Commands BED2SGA(1)

bed2sga - Convert BED format into SGA format.

bed2sga [options] [-s <s_assembly (e.g. hg19)>] [<] <BED file|stdin>

- version 1.5.5 where options are:
Produce Debug information
Show this Help text
Use <path> to locate the assembly-specific chr_NC_gi file [default is: $HOME/db/genome]
Set Feature name <ft>
Assembly <spec> (i.e hg19)
Generate a Centered SGA file
Generate an unoriented SGA file
Generate a 2-line[+/-] SGA file representing BED regions (e.g. RepeatMasker regions)
Produce an extended SGA file with additional fields specified by a comma-separated list of BED column numbers (from 1 to n)
Use the BED 'score' field (#5) to set the SGA 'count' field
Use the BED 'Signal Value' field (#7) to set the SGA 'count' field [This option is only valid for ENCODE narrowPeak]
Use this option for ENCODE narrowPeak format [Options --useScore, -c, and -u are ignored]
Convert BED format into SGA format.


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