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  Long-read transcriptome sequencing analysis with IsoTools

Lienhard, M., van den Beucken, T., Timmermann, B., Hochradel, M., Boerno, S., Caiment, F., et al. (2021). Long-read transcriptome sequencing analysis with IsoTools. bioRxiv. doi:10.1101/2021.07.13.452091.

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Lienhard, Matthias1, Author              
van den Beucken, Twan, Author
Timmermann, Bernd2, Author              
Hochradel, Myriam2, Author              
Boerno, Stefan2, Author              
Caiment, Florian , Author
Vingron, Martin3, Author              
Herwig, Ralf1, Author              
Affiliations:
1Bioinformatics (Ralf Herwig), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_2385701              
2Sequencing Core Facility (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479670              
3Transcriptional Regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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 Abstract: Long-read transcriptome sequencing (LRTS) holds the promise to boost our understanding of alternative splicing. Recent advances in accuracy and throughput have diminished the major limitations and enabled the direct quantification of isoforms. Considering the complexity of the data and the broad range of potential applications, it is clear that highly flexible, accurate analysis tools are crucial. Here, we present IsoTools, a comprehensive Python-based analysis package, for the improvement of alternative and differential splicing analysis. Iso-Tools provides a comprehensive data structure that integrates genomic information from LRTS transcripts together with the reference annotation, and enables broad functionality to quality control, visualize and analyze the data. Additionally, we implemented a graph-based method for the identification of alternative splicing events and a statistical approach based on the beta binomial distribution for the detection of differential events. To demonstrate our methods, we generated PacBio Iso-Seq data of human hepatocytes treated with the HDAC inhibitor valproic acid, a compound known to induce widespread transcriptional changes. Contrasted with short read RNA-Seq of the same samples, this analysis shows that LRTS provides valuable additional insights for a better understanding of alternative splicing, in particular with respect to complex novel and differential splicing events. IsoTools is made available for the community along with extensive documentation at https://github.com/MatthiasLienhard/isotools.

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Language(s): eng - English
 Dates: 2021-07-14
 Publication Status: Published online
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 Identifiers: DOI: 10.1101/2021.07.13.452091
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Title: bioRxiv
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