.TH INSEGT 1 "" "insegt 1.1.9 [tarball]" ""
.SH NAME
insegt \- INtersecting SEcond Generation sequencing daTa with annotation
.SH SYNOPSIS
\fBinsegt\fP [\fIOPTIONS\fP] <\fIALIGMENTS-FILE\fP> <\fIANNOTATIONS-FILE\fP> 
.SH DESCRIPTION
INSEGT is a tool to analyze alignments of RNA-Seq reads (single-end or paired-end) by using gene-annotations.
.sp
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.
.SH REQUIRED ARGUMENTS
.TP
\fBARGUMENT 0\fP \fIINPUT_FILE\fP
 Valid filetype is: \fI.sam\fP.
.TP
\fBARGUMENT 1\fP \fIINPUT_FILE\fP
 Valid filetypes are: \fI.gtf\fP and \fI.gff\fP.
.SH OPTIONS
.TP
\fB-h\fP, \fB--help\fP
Display the help message.
.TP
\fB--version\fP
Display version information.
.SS Options: :
.TP
\fB-ro\fP, \fB--read-output\fP \fIOUTPUT_FILE\fP
Output filename for read-output, which contains the mapped annotations followed by their parent annotation. Valid filetype is: \fI.gff\fP.
.TP
\fB-ao\fP, \fB--anno-output\fP \fIOUTPUT_FILE\fP
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: \fI.gff\fP.
.TP
\fB-to\fP, \fB--tuple-output\fP \fIOUTPUT_FILE\fP
Output filename for tuple-output, which contains exon tuples connected by reads or matepairs. Valid filetype is: \fI.gff\fP.
.TP
\fB-fo\fP, \fB--fusion-output\fP \fISTRING\fP
Output filename for fusion-output, which contains exon tuple of gene fusions (Advanced option, currently no output port for KNIME). One of \fIgff\fP.
.TP
\fB-n\fP, \fB--ntuple\fP \fIINTEGER\fP
ntuple Default: \fI2\fP.
.TP
\fB-o\fP, \fB--offset-interval\fP \fIINTEGER\fP
Offset to short alignment-intervals for search. Default: \fI5\fP.
.TP
\fB-t\fP, \fB--threshold-gaps\fP \fIINTEGER\fP
Threshold for allowed gaps in alignment (not introns). Default: \fI5\fP.
.TP
\fB-c\fP, \fB--threshold-count\fP \fIINTEGER\fP
Threshold for min. count of tuple for output. Default: \fI1\fP.
.TP
\fB-r\fP, \fB--threshold-rpkm\fP \fIDOUBLE\fP
Threshold for min. RPKM of tuple for output. Default: \fI0.0\fP.
.TP
\fB-m\fP, \fB--max-tuple\fP
Create only maxTuple (which are spanned by the whole read).
.TP
\fB-e\fP, \fB--exact-ntuple\fP
Create only Tuple of exact length n. By default all tuple up to the given length are computed (if -m is set, -e will be ignored).
.TP
\fB-u\fP, \fB--unknown-orientation\fP
Orientation of reads is unknown.
.SH EXAMPLES
.TP
\fBinsegt\fP  \fBexample/alignments.sam\fP \fBexample/annotations.gff\fP
Run INSEGT on example files with default parameters.
.TP
\fBinsegt\fP \fB-m\fP \fBexample/alignments.sam\fP \fBexample/annotations.gff\fP
Run INSEGT on example files and only compute maxTuple.
.TP
\fBinsegt\fP \fB-c\fP \fB2\fP \fBexample/alignments.sam\fP \fBexample/annotations.gff\fP
Run INSEGT on example files and only output tuple with a min. count of 2.