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

Cloonan, Nicole; Xu, Qinying; Faulkner, Geoffrey J; Taylor, Darrin F; Tang, Dave T P; Kolle, Gabriel; Grimmond, Sean M.
Bioinformatics; 25(19): 2615-6, 2009 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-19648138
UNLABELLED: 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/
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