NGS technologies allow to produce millions of reads, e.g. coming from expressed RNAs of a cell (RNA-Seq). INSEGT is a tool to analyse alignments of RNA-Seq reads (single-end or paired-end) by using gene annotations. It can measure exon, transcript and gene expression levels of given annotations. If read alignments span more than one exon, INSEGT can also compute possible exon combinations (tuple) and their expression levels. According to requirements it computes maximal tuple or tuple with a certain length. For paired-end reads INSEGT builds also tuple, whose exons are connected by matepairs. Briefly it searches the intervals of the read alignments in the intervals of the given annotations. It counts the mapped reads for each annotation and its parent annotation and stores the mapped annotations for each read.

INSEGT produces three output files: The first contains the expression levels of the given annotations. The second contains for each given read the mapped annotations. If the read mapped in not annotated regions, an UNKNOWN_REGION in the output will mark this. And the third file contains exon-tuple and their expression levels.

Additional Online Material

Also see the README file for more information.

Version History

2009-10-22: v1.0

  • First version of INSEGT


Follow the Getting Started section and check out the latest SVN trunk. Instead of creating a project file in Debug mode, switch to Release mode (-DCMAKE_BUILD_TYPE=Release) and compile insegt. This can be done as follows:

svn co seqan-trunk
mkdir seqan-trunk-build
cd seqan-trunk-build/
cmake ../../seqan-trunk -DCMAKE_BUILD_TYPE=Release
make insegt
./extras/apps/insegt/insegt --help


For questions, comments, or suggestions feel free to contact David Weese or Sabrina Krakau.


  1. Krakau, S.(2009). INSEGT: Ein Programm für annotationsbasierte Expressionanalyse von RNA-Seq Daten.
Last Update 7. May 2013