TappAS: a Comprehensive Computational Framework for the Analysis of the Functional Impact of Differential Splicing

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2020 May 20

PMID 32423416

Citations 32

Authors

Lorena de la Fuente

Angeles Arzalluz-Luque

Manuel Tardaguila

Hector Del Risco

Cristina Marti

Sonia Tarazona

Pedro Salguero

Raymond Scott

Alberto Lerma

Ana Alastrue-Agudo

Pablo Bonilla

Jeremy R B Newman

Shunichi Kosugi

Lauren M McIntyre

Victoria Moreno-Manzano

Ana Conesa

Affiliations

Soon will be listed here.

Abstract

Recent advances in long-read sequencing solve inaccuracies in alternative transcript identification of full-length transcripts in short-read RNA-Seq data, which encourages the development of methods for isoform-centered functional analysis. Here, we present tappAS, the first framework to enable a comprehensive Functional Iso-Transcriptomics (FIT) analysis, which is effective at revealing the functional impact of context-specific post-transcriptional regulation. tappAS uses isoform-resolved annotation of coding and non-coding functional domains, motifs, and sites, in combination with novel analysis methods to interrogate different aspects of the functional readout of transcript variants and isoform regulation. tappAS software and documentation are available at https://app.tappas.org.

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