.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.1.
.TH INSEGT "1" "September 2014" "insegt 1.4.1+dfsg" "User Commands"
.SH NAME
insegt \- INtersecting SEcond Generation sequencing daTa with annotation
.PP
SYNOPSIS
.IP
insegt [OPTIONS] <ALIGMENTS\-FILE> <ANNOTATIONS\-FILE>
.PP
DESCRIPTION
.IP
INSEGT is a tool to analyze alignments of RNA\-Seq reads (single\-end or
paired\-end) by using gene\-annotations.
.IP
Input to INSEGT is a SAM file containing the alignments and a file
containing the annotations of the reference genome, either in GFF or GTF
format.
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Displays this help message.
.HP
\fB\-\-version\fR
.IP
Display version information
.IP
Options: :
.HP
\fB\-ro\fR, \fB\-\-read\-output\fR FILE
.IP
Output filename for read\-output, which contains the mapped
annotations followed by their parent annotation. Valid filetype is:
gff.
.HP
\fB\-ao\fR, \fB\-\-anno\-output\fR FILE
.IP
Output filename for anno\-output, which contains the annotations
similar to the GFF input and additionally the counts of the mapped
reads and the normalized expression levels in RPKM. Valid filetype
is: gff.
.HP
\fB\-to\fR, \fB\-\-tuple\-output\fR FILE
.IP
Output filename for tuple\-output, which contains exon tuples
connected by reads or matepairs. Valid filetype is: gff.
.HP
\fB\-fo\fR, \fB\-\-fusion\-output\fR STR
.IP
Output filename for fusion\-output, which contains exon tuple of gene
fusions (Advanced option, currently no output port for KNIME). One
of gff.
.HP
\fB\-n\fR, \fB\-\-ntuple\fR INT
.IP
ntuple Default: 2.
.HP
\fB\-o\fR, \fB\-\-offset\-interval\fR INT
.IP
Offset to short alignment\-intervals for search. Default: 5.
.HP
\fB\-t\fR, \fB\-\-threshold\-gaps\fR INT
.IP
Threshold for allowed gaps in alignment (not introns). Default: 5.
.HP
\fB\-c\fR, \fB\-\-threshold\-count\fR INT
.IP
Threshold for min. count of tuple for output. Default: 1.
.HP
\fB\-r\fR, \fB\-\-threshold\-rpkm\fR DOUBLE
.IP
Threshold for min. RPKM of tuple for output. Default: 0.0.
.HP
\fB\-m\fR, \fB\-\-max\-tuple\fR
.IP
Create only maxTuple (which are spanned by the whole read).
.HP
\fB\-e\fR, \fB\-\-exact\-ntuple\fR
.IP
Create only Tuple of exact length n. By default all tuple up to the
given length are computed (if \fB\-m\fR is set, \fB\-e\fR will be ignored).
.HP
\fB\-u\fR, \fB\-\-unknown\-orientation\fR
.IP
Orientation of reads is unknown.
.PP
EXAMPLES
.TP
insegt
example/alignments.sam example/annotations.gff
.IP
Run INSEGT on example files with default parameters.
.IP
insegt \fB\-m\fR example/alignments.sam example/annotations.gff
.IP
Run INSEGT on example files and only compute maxTuple.
.IP
insegt \fB\-c\fR 2 example/alignments.sam example/annotations.gff
.IP
Run INSEGT on example files and only output tuple with a min. count
of 2.
.PP
VERSION
.IP
insegt version: 1.0
Last update 2012\-09\-11