A survey of software for genome-wide discovery of differential splicing in RNA-Seq dataReport as inadecuate




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Human Genomics

, 8:3

First Online: 21 January 2014Received: 02 September 2013Accepted: 26 December 2013

Abstract

Alternative splicing is a major contributor to cellular diversity. Therefore the identification and quantification of differentially spliced transcripts in genome-wide transcript analysis is an important consideration. Here, I review the software available for analysis of RNA-Seq data for differential splicing and discuss intrinsic challenges for differential splicing analyses. Three approaches to differential splicing analysis are described, along with their associated software implementations, their strengths, limitations, and caveats. Suggestions for future work include more extensive experimental validation to assess accuracy of the software predictions and consensus formats for outputs that would facilitate visualizations, data exchange, and downstream analyses.

KeywordsRNA-Seq Software Differential splicing Alternative splicing Splicing analysis AbbreviationsASAlternative splicing

ASMsAlternative splicing modules

fdrFalse discovery rate

PSIPercent spliced in

qRT-PCRQuantitative reverse transcribed-polymerase chain reaction

UTRsUntranslated regions.

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Author: Joan E Hooper

Source: https://link.springer.com/



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