Dataset Information
RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data.
Ontology highlight
ABSTRACT: 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/
SUBMITTER: Cloonan N
PROVIDER: S-EPMC2752615 | biostudies-literature | 2009 Oct
REPOSITORIES: biostudies-literature
Publications
RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data.
Bioinformatics (Oxford, England) 20090730 19
<h4>Unlabelled</h4>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 mappa ...[more]