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.
We also offer a web-application for TSSpredator that besides the TSS identification, it allows the visualization of the results.
Visit TSSpredator-Web at https://tsspredator-tuevis.cs.uni-tuebingen.de/
GitHub: https://github.com/Integrative-Transcriptomics/TSSpredator-GUI
For the offline version:
TSSpredator is free for academic use. The current TSSpredator version 1.1beta (March 2021) offers the following improvements:
- Improved file coherence
- Annotation files in GTF/GFF supported
- User-specified output ID field for TSS classification
For the user guide for TSSpredator V1.1, see here. This guide also includes two tutorials to learn how to use TSSpredator. The topics covered in these tutorials are multi-strain analysis as well as comparison of conditions. The example data used in the tutorials can be downloaded from here.
Contact
For questions and bug reports, please contact Kay Nieselt.
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