In:
Current Protocols in Bioinformatics, Wiley, Vol. 32, No. 1 ( 2010-12)
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. Curr. Protoc. Bioinform . 32:11.6.1‐11.6.37. © 2010 by John Wiley & Sons, Inc.
Type of Medium:
Online Resource
ISSN:
1934-3396
,
1934-340X
DOI:
10.1002/0471250953.2010.32.issue-1
DOI:
10.1002/0471250953.bi1106s32
Language:
English
Publisher:
Wiley
Publication Date:
2010
detail.hit.zdb_id:
2179022-X
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