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.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Pruitt KD, Tatusova T, Maglott DR (2005) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 33:501–504
Curwen V, Eyras E, Andrews TD, Clarke L, Mongin E, Searle SM, Clamp M (2004) The Ensembl automatic gene annotation system. Genome Res 14:942–950
Au KF, Jiang H, Lin L, Xing Y, Wong WH (2010) Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res 38:4570–4578
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
Jiang H, Wong WH (2008) SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24:2395–2396
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Au, K.F. (2015). Accurate Mapping of RNA-Seq Data. In: Picardi, E. (eds) RNA Bioinformatics. Methods in Molecular Biology, vol 1269. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2291-8_9
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2291-8_9
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2290-1
Online ISBN: 978-1-4939-2291-8
eBook Packages: Springer Protocols