UNIT 11.6 RNA-Seq Read Alignments with PALMapper

  1. Géraldine Jean,
  2. André Kahles,
  3. Vipin T. Sreedharan,
  4. Fabio De Bona,
  5. Gunnar Rätsch

Published Online: 1 DEC 2010

DOI: 10.1002/0471250953.bi1106s32

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Jean, G., Kahles, A., Sreedharan, V. T., Bona, F. D. and Rätsch, G. 2010. RNA-Seq Read Alignments with PALMapper. Current Protocols in Bioinformatics. 32:11.6:11.6.1–11.6.37.

Author Information

  1. Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany

Publication History

  1. Published Online: 1 DEC 2010
  2. Published Print: DEC 2010


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.


  • RNA-Seq;
  • sequence alignment;
  • splice-site prediction;
  • PALMapper;
  • GenomeMapper;
  • Galaxy