FESTA: Flexible Exon-based Splicing and Transcription Annotation
We introduce FESTA, an R based algorithm that allows detection of alternative splicing based on experiment-specific exon expression data. FESTA disentangles alternative splicing signal from whole-gene transcription, facilitating the discovery and characterization of novel regulatory events even in t...
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| Published in | bioRxiv |
|---|---|
| Main Authors | , |
| Format | Paper |
| Language | English |
| Published |
Cold Spring Harbor
Cold Spring Harbor Laboratory Press
17.04.2018
Cold Spring Harbor Laboratory |
| Edition | 1.1 |
| Subjects | |
| Online Access | Get full text |
| ISSN | 2692-8205 2692-8205 |
| DOI | 10.1101/300947 |
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| Abstract | We introduce FESTA, an R based algorithm that allows detection of alternative splicing based on experiment-specific exon expression data. FESTA disentangles alternative splicing signal from whole-gene transcription, facilitating the discovery and characterization of novel regulatory events even in the absence of transcript annotations or paired-end data. We also include customization options to increase its applicability on different platforms and experimental designs as well as a tool for the conversion from transcript expression to inclusion ratios. |
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| AbstractList | We introduce FESTA, an R based algorithm that allows detection of alternative splicing based on experiment-specific exon expression data. FESTA disentangles alternative splicing signal from whole-gene transcription, facilitating the discovery and characterization of novel regulatory events even in the absence of transcript annotations or paired-end data. We also include customization options to increase its applicability on different platforms and experimental designs as well as a tool for the conversion from transcript expression to inclusion ratios. |
| Author | Colbourne, John Kenneth Rago, Alfredo |
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| Copyright | 2018. This article is published under http://creativecommons.org/licenses/by-nc/4.0/ ( the License ). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2018, Posted by Cold Spring Harbor Laboratory |
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| DOI | 10.1101/300947 |
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| References | Chen (300947v1.1) 2013; 15 McManus, Coolon, Eipper-Mains, Wittkopp, Graveley (300947v1.3) 2014; 24 Patrick, Buckley, Yang (300947v1.4) 2013; 14 Trapnell, Williams, Pertea, Mortazavi, Kwan, van Baren, Salzberg, Wold, Pachter (300947v1.5) 2010; 28 Dai, Li, Liu, Zhou (300947v1.2) 2012; 6 |
| References_xml | – volume: 6 start-page: S17 issue: 1 year: 2012 ident: 300947v1.2 article-title: Integrating many co-splicing networks to reconstruct splicing regulatory modules publication-title: BMC systems biology – volume: 15 start-page: 542 issue: 4 year: 2013 end-page: 551 ident: 300947v1.1 article-title: Are all of the human exons alternatively spliced? publication-title: Briefings in bioinformatics – volume: 14 start-page: 31 year: 2013 ident: 300947v1.4 article-title: Estimation of data-specific constitutive exons with RNA-Seq data publication-title: BMC bioinformatics – volume: 24 start-page: 786 issue: 5 year: 2014 end-page: 96 ident: 300947v1.3 article-title: Evolution of splicing regulatory networks in Drosophila publication-title: Genome research – volume: 28 start-page: 511 issue: 5 year: 2010 end-page: 5 ident: 300947v1.5 article-title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation publication-title: Nature biotechnology |
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| Title | FESTA: Flexible Exon-based Splicing and Transcription Annotation |
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