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Bioinformatics. 2019 Oct 16. pii: btz784. doi: 10.1093/bioinformatics/btz784. [Epub ahead of print]

SpliceLauncher: a tool for detection, annotation and relative quantification of alternative junctions from RNAseq data.

Author information

1
Laboratoire de biologie et de génétique du cancer, Centre François Baclesse, Caen, France.
2
Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.
3
Normandie Univ, UNICAEN, Caen, France.
4
Cancéropôle Nord-Ouest Data Processing Centre, CLCC François Baclesse, Caen, France.
5
Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France.
6
Hub Bioinformatique et Biostatistique, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France.
7
GenoSplice technology, Paris, France.
8
Gustave Roussy, Université Paris-Saclay, Département de Biopathologie, Villejuif, France.

Abstract

SUMMARY:

Alternative splicing is an important biological process widely analyzed in molecular diagnostic settings. Indeed, a variant can be pathogenic by splicing alteration and a suspected pathogenic variant (e.g. truncating variant) can be rescued by splicing. In this context, detecting and quantifying alternative splicing is challenging. We developed SpliceLauncher, a fast and easy to use open source tool that aims at detecting, annotating and quantifying alternative splice junctions at high resolution.

AVAILABILITY:

SpliceLauncher is available at https://github.com/raphaelleman/SpliceLauncher.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

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