| Chapter title |
Accurate Mapping of RNA-Seq Data.
|
|---|---|
| Chapter number | 9 |
| Book title |
RNA Bioinformatics
|
| Published in |
Methods in molecular biology, December 2014
|
| DOI | 10.1007/978-1-4939-2291-8_9 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-2290-1, 978-1-4939-2291-8
|
| Authors |
Au KF, Kin Fai Au |
| Editors |
Ernesto Picardi |
| Abstract |
The mapping of RNA-Seq data on genome is not the same as DNA-Seq data, because the junction reads span two exons and have no identical matches at reference genome. In this chapter, we describe a junction read aligner SpliceMap that is based on an algorithm of "half-read seeding" and "seeding extension." Four analysis steps are integrated in SpliceMap (half-read mapping, seeding selection, seeding extension and junction search, and paired-end filtering), and all toning parameters of these steps can be editable in a single configuration file. Thus, SpliceMap can be executed by a single command. While we describe the analysis steps of SpliceMap, we illustrate how to choose the parameters according to the research interest and RNA-Seq data quality by an example of human brain RNA-Seq data. |
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