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Bioinformatics Advance Access originally published online on July 30, 2009
Bioinformatics 2009 25(19):2615-2616; doi:10.1093/bioinformatics/btp459
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data

Nicole Cloonan *,{dagger}, Qinying Xu {dagger}, Geoffrey J. Faulkner , Darrin F. Taylor , Dave T. P. Tang , Gabriel Kolle and Sean M. Grimmond

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, Australia

*To whom correspondence should be addressed.


  Abstract

Summary: Mapping of next-generation sequencing data derived from RNA samples (RNAseq) presents different genome mapping challenges than data derived from DNA. For example, tags that cross exon-junction boundaries will often not map to a reference genome, and the strand specificity of the data needs to be retained. Here we present RNA-MATE, a computational pipeline based on a recursive mapping strategy for placing strand specific RNAseq data onto a reference genome. Maximizing the mappable tags can provide significant savings in the cost of sequencing experiments. This pipeline provides an automatic and integrated way to align color-space sequencing data, collate this information and generate files for examining gene-expression data in a genomic context.

Availability: Executables, source code, and exon-junction libraries are available from http://grimmond.imb.uq.edu.au/RNA-MATE/

Contact: n.cloonan{at}imb.uq.edu.au

Supplementary information: Supplementary data are available at Bioinformatics Online.

Associate Editor: Joaquin Dopazo

{dagger} The authors wish it be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Received on February 4, 2009; revised on July 21, 2009; accepted on July 22, 2009

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