TECtool specifications

Information


Unique identifier OMICS_31996
Name TECtool
Alternative name Terminal Exon Characterization tool
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A file containing all chromosomes, a file with the corresponding annotation, a file with genome coordinates of 3’ end processing sites and a file containing spliced alignments of mRNA-seq reads to the corresponding genome.
Input format FASTA+GTF+BED+BAM
Output data An augmented annotation file, a file containing the novel terminal exons, a file containing the root and the novel transcript ids and an optionnal directory.
Output format GTF+TSV
Operating system Unix/Linux, Mac OS
Programming languages Python
License MIT License
Computer skills Advanced
Version 0.4
Stability Stable
Requirements
numpy, htseq, pybedtools, pyfasta, scikit-learn, pandas, matplotlib, scipy, progress
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Mihaela Zavolan

Additional information


https://git.scicore.unibas.ch/zavolan_public/TECtool

Publication for Terminal Exon Characterization tool

TECtool institution(s)
Oxford Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
TECtool funding source(s)
Supported by the Swiss National Science Foundation (grants 31003A_170216 and 51NF40_141735 (National Center for Competence in Research ‘RNA & Disease’; to the NCCR consortium)) and the Marie Curie Initial Training Network (project #607720, RNATRAIN).

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