---
name: "insegt"
section: "1"
platform: "linux"
package: "seqan-apps"
version: "2.4.0+dfsg-16"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/insegt"
---

# insegt(1)

INtersecting SEcond Generation sequencing daTa with annotation

## NAME

insegt - INtersecting SEcond Generation sequencing daTa with annotation

## SYNOPSIS

**insegt** \[*OPTIONS*\] \<*ALIGMENTS-FILE*\> \<*ANNOTATIONS-FILE*\>

## DESCRIPTION

INSEGT is a tool to analyze alignments of RNA-Seq reads (single-end or paired-end) by using gene-annotations.

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.

## REQUIRED ARGUMENTS

- **ARGUMENT 0** *INPUT\_FILE*

   Valid filetype is: *.sam*.

- **ARGUMENT 1** *INPUT\_FILE*

   Valid filetypes are: *.gtf* and *.gff*.

## OPTIONS

- **-h**, **--help**

  Display the help message.

- **--version**

  Display version information.

### Options: :

- **-ro**, **--read-output** *OUTPUT\_FILE*

  Output filename for read-output, which contains the mapped annotations followed by their parent annotation. Valid filetype is: *.gff*.

- **-ao**, **--anno-output** *OUTPUT\_FILE*

  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*.

- **-to**, **--tuple-output** *OUTPUT\_FILE*

  Output filename for tuple-output, which contains exon tuples connected by reads or matepairs. Valid filetype is: *.gff*.

- **-fo**, **--fusion-output** *STRING*

  Output filename for fusion-output, which contains exon tuple of gene fusions (Advanced option, currently no output port for KNIME). One of *gff*.

- **-n**, **--ntuple** *INTEGER*

  ntuple Default: *2*.

- **-o**, **--offset-interval** *INTEGER*

  Offset to short alignment-intervals for search. Default: *5*.

- **-t**, **--threshold-gaps** *INTEGER*

  Threshold for allowed gaps in alignment (not introns). Default: *5*.

- **-c**, **--threshold-count** *INTEGER*

  Threshold for min. count of tuple for output. Default: *1*.

- **-r**, **--threshold-rpkm** *DOUBLE*

  Threshold for min. RPKM of tuple for output. Default: *0.0*.

- **-m**, **--max-tuple**

  Create only maxTuple (which are spanned by the whole read).

- **-e**, **--exact-ntuple**

  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).

- **-u**, **--unknown-orientation**

  Orientation of reads is unknown.

## EXAMPLES

- **insegt** **example/alignments.sam** **example/annotations.gff**

  Run INSEGT on example files with default parameters.

- **insegt** **-m** **example/alignments.sam** **example/annotations.gff**

  Run INSEGT on example files and only compute maxTuple.

- **insegt** **-c** **2** **example/alignments.sam** **example/annotations.gff**

  Run INSEGT on example files and only output tuple with a min. count of 2.