Please note: RNA-MATE has now been superseded by X-MATE

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

Nicole Cloonan, Qinying Xu, Geoffrey J. Faulkner, Darrin F. Taylor, Dave T.P. Tang, and Sean M. Grimmond

Bioinformatics 2009, 25(19):2615-2616
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Abstract

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. 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.

Supplementary Material

Supplementary Table 1. The level of rescue achieved for low and high complexity libraries (PDF, 8.7KB). [Click Here]

Previous Versions

The latest version of RNA-MATE is v1.1

RNA-MATEv1.01

RNA-MATEv1.0