title: RNA-Seq read alignments with PALMapper.
abstract: Next-generation sequencing technologies have revolutionized genome and transcriptome sequencing. RNA-Seq experiments are able to generate huge amounts of transcriptome sequence reads at a fraction of the cost of Sanger sequencing. Reads produced by these technologies are relatively short and error prone. To utilize such reads for transcriptome reconstruction and gene-structure identification, one needs to be able to accurately align the sequence reads over intron boundaries. In this unit, we describe PALMapper, a fast and easy-to-use tool that is designed to accurately compute both unspliced and spliced alignments for millions of RNA-Seq reads. It combines the efficient read mapper GenomeMapper with the spliced aligner QPALMA, which exploits read-quality information and predictions of splice sites to improve the alignment accuracy. The PALMapper package is available as a command-line tool running on Unix or Mac OS X systems or through a Web interface based on Galaxy tools.
authors.affiliation: Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany.
authors.forename: Géraldine
authors.initials: G
authors.lastname: Jean
authors.forename: André
authors.initials: A
authors.lastname: Kahles
authors.forename: Vipin T
authors.initials: VT
authors.lastname: Sreedharan
authors.forename: Fabio
authors.initials: F
authors.lastname: De Bona
authors.forename: Gunnar
authors.initials: G
authors.lastname: Rätsch
mesh_terms: D001483:Base Sequence; D020869:Gene Expression Profiling; D016678:Genome; D023281:Genomics / Q000379:methods*; D012313:RNA / Q000737:chemistry*; D012326:RNA Splicing; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA