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, Advance Online Publication
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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]
The current version of RNA-MATE is v1.1
- RNA-MATE user manual. Preliminary documentation (PDF, 1.8MB). [Click Here]
- RNA-MATE source code. Modules and executables for RNA-MATE (tar.gz, 85K). [Click Here]
- Junction Libraries. Exon-junction libraries used in Nature Methods (2008) 5:613-619 (tar.gz, 46MB). [Click Here]
- Junction Libraries. Exon-junction libraries based on UCSC genes and gene-models (tar.gz, 386MB). [Click Here]
- Testing data. SOLiD test data and configuration files (tar.gz 9.1MB). [Click Here]
- Testing results. Test results, wiggle plots and BED files (tar.gz 7.5MB). [Click Here]
Previous Versions
RNA-MATEv1.01
- RNA-MATE source code. Modules and executables for RNA-MATEv1.01 (tar.gz, 83K). [Click Here]
- RNA-MATE user manual. Preliminary documentation (PDF, 142KB). [Click Here]
RNA-MATEv1.0
- RNA-MATE source code. Modules and executables for RNA-MATEv1.0 (tar.gz, 19K). [Click Here]
- RNA-MATE user manual. Preliminary documentation (PDF, 139KB). [Click Here]