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RNA-Seq Read Alignments with PALMapper.
Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit11.6
Authors: Jean G, Kahles A, Sreedharan VT, Bona FD, Rätsch G
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.Curr. Protoc. Bioinform. 32:11.6.1-11.6.37. © 2010 by John Wiley & Sons, Inc.
PMID: 21154708 [PubMed - as supplied by publisher]
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RNA-Seq Read Alignments with PALMapper.
Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit11.6
Authors: Jean G, Kahles A, Sreedharan VT, Bona FD, Rätsch G
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.Curr. Protoc. Bioinform. 32:11.6.1-11.6.37. © 2010 by John Wiley & Sons, Inc.
PMID: 21154708 [PubMed - as supplied by publisher]
More...
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