Chapter title |
NGS-Trex: An Automatic Analysis Workflow for RNA-Seq Data
|
---|---|
Chapter number | 15 |
Book title |
RNA Bioinformatics
|
Published in |
Methods in molecular biology, December 2014
|
DOI | 10.1007/978-1-4939-2291-8_15 |
Pubmed ID | |
Book ISBNs |
978-1-4939-2290-1, 978-1-4939-2291-8
|
Authors |
Ilenia Boria, Lara Boatti, Igor Saggese, Flavio Mignone |
Editors |
Ernesto Picardi |
Abstract |
RNA-Seq technology allows the rapid analysis of whole transcriptomes taking advantage of next-generation sequencing platforms. Moreover with the constant decrease of the cost of NGS analysis RNA-Seq is becoming very popular and widespread. Unfortunately data analysis is quite demanding in terms of bioinformatic skills and infrastructures required, thus limiting the potential users of this method.Here we describe the complete analysis of sample data from raw sequences to data mining of results by using NGS-Trex platform, a low user interaction, fully automatic analysis workflow. Used through a web interface, NGS-Trex processes data and profiles the transcriptome of the samples identifying expressed genes, transcripts, and new and known splice variants. It also detects differentially expressed genes and transcripts across different experiments. |
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Unknown | 1 | 100% |
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Members of the public | 1 | 100% |
Mendeley readers
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Researcher | 5 | 26% |
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Student > Bachelor | 1 | 5% |
Student > Doctoral Student | 1 | 5% |
Other | 1 | 5% |
Unknown | 2 | 11% |
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Computer Science | 1 | 5% |
Environmental Science | 1 | 5% |
Other | 0 | 0% |
Unknown | 3 | 16% |