.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH SGA2BED "1" "March 2020" "sga2bed 1.5.5" "User Commands"
.SH NAME
sga2bed \- Convert SGA format into BED format
.SH SYNOPSIS
.B sga2bed
[\fI\,options\/\fR] [\fI\,<\/\fR] \fI\,<SGA 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 chr_NC_gi file
[default is: $HOME/db/genome]
.TP
\fB\-l\fR|\-\-readlen <len>
Set Read length <len>
Unoriented SGA files are extended by +/\-<len>/2
.TP
\fB\-c\fR|\-\-score <score>
Normalisation factor for BED score field (5th) [score=1]
.TP
\fB\-n\fR|\-\-norm
<normf>        Normalisation factor for BED score field (7th) [normf=1]
.TP
\fB\-e\fR|\-\-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
.TP
\fB\-r\fR|\-\-nohdr
BED format without annotation track header lines
.TP
\fB\-x\fR|\-\-expand
Expand SGA lines into multiple BED lines
.TP
\fB\-\-name\fR <name>
Set name for track name field [def. name=SGA\-feature]
.TP
\fB\-\-desc\fR <desc>
Set track description field [def. desc="ChIP\-Seq Custom data"]
.TP
\fB\-\-color\fR <col>
Define the track color in comma\-separated RGB values [def. 100,100,100]
.IP
Convert SGA format into BED 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.