.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH BED2SGA "1" "March 2020" "bed2sga 1.5.5" "User Commands"
.SH NAME
bed2sga \- Convert BED format into SGA format.
.SH SYNOPSIS
.B bed2sga
[\fI\,options\/\fR] [\fI\,-s <s_assembly (e.g. hg19)>\/\fR] [\fI\,<\/\fR] \fI\,<BED file|stdin>\/\fR
.SH DESCRIPTION
.IP
\- version 1.5.5
where options are:
.TP
\fB\-d\fR|\-\-debug
Produce Debug information
.TP
\fB\-h\fR|\-\-help
Show this Help text
.TP
\fB\-i\fR|\-\-db <path>
Use <path> to locate the assembly\-specific chr_NC_gi file
[default is: $HOME/db/genome]
.TP
\fB\-f\fR|\-\-feature <ft>
Set Feature name <ft>
.TP
\fB\-s\fR|\-\-species <spec>
Assembly <spec> (i.e hg19)
.TP
\fB\-c\fR|\-\-center
Generate a Centered SGA file
.TP
\fB\-u\fR|\-\-unoriented
Generate an unoriented SGA file
.TP
\fB\-r\fR|\-\-regional
Generate a 2\-line[+/\-] SGA file representing BED regions
(e.g. RepeatMasker regions)
.TP
\fB\-e\fR|\-\-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)
.TP
\fB\-\-useScore\fR
Use the BED 'score' field (#5) to set the SGA 'count' field
.TP
\fB\-\-useSigVal\fR
Use the BED 'Signal Value' field (#7) to set the SGA 'count' field
[This option is only valid for ENCODE narrowPeak]
.TP
\fB\-\-narrowPeak\fR
Use this option for ENCODE narrowPeak format
[Options \fB\-\-useScore\fR, \fB\-c\fR, and \fB\-u\fR are ignored]
.IP
Convert BED format into SGA format.
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.