Software


TSSpredator

RNA deep-sequencing technologies (RNA-seq) are able to provide detailed insights into the transcriptomic structures of eukaryotic and prokaryotic organisms. This includes the genome-wide detection of transcription start sites (TSS).
Manual annotation of TSS is laborious and time intensive and becomes infeasible when comparing different species.
We therefore developed TSSpredator, a Java program for the automated detection and classification of TSS from RNA-seq data.
TSSpredator reads RNA-seq data in the form of simple wiggle files and performs a genome wide comparative prediction of TSS, for example between different growth conditions.
For the comparison of different organisms we integrated the SuperGenome approach which generates a common coordinate system for the compared genomes, allowing the comparative annotation of TSS across several species.
TSSpredator provides a user-friendly interface which allows for the setting of all necessary parameters. By this all aspects of the prediction procedure can be customized. However, the program also provides several parameter presets for a quick application of the program.
In addition, TSSpredator can also be utilized via a command line interface for the easy integration into automated data analysis pipelines.


Citation

Related publications:

Dugar G, Herbig A, Förstner KU, Heidrich N, Reinhardt R, Nieselt K, Sharma CM.
High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates.
PLoS Genet. 2013 May ; 9(5): e1003495


Download

TSSpredator is free for academic use.

March 17, 2017

May 31, 2016

  • Open beta: TSSpredator 1.07beta (introduces multiple
    contig/chromosome support and a more robust enrichment factor
    normalization. Note: This version is still in development, so if you
    do not need multiple contig or chromosome support, please work with
    version 1.06)

February 17, 2016

Older versions of TSSpredator can be downloaded here.

The User Guide for TSSpredator v. 1.06 can be downloaded from here.

Example data can be downloaded here.


Contact

For questions and bug reports please contact
Kay Nieselt or
Alexander Herbig.