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

@article{citeulike:5308811, 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@imb.uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics Online. 10.1093/bioinformatics/btp459}, author = {Cloonan, Nicole and Xu, Qinying and Faulkner, Geoffrey J. and Taylor, Darrin F. and Tang, Dave T. P. and Kolle, Gabriel and Grimmond, Sean M.}, citeulike-article-id = {5308811}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp459}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/25/19/2615.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/25/19/2615.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19648138}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19648138}, day = {1}, doi = {10.1093/bioinformatics/btp459}, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {data, high-throughput, mapping, recursive, rna, rna-seq, sequencing, strategy}, month = {October}, number = {19}, pages = {2615--2616}, posted-at = {2009-09-28 09:47:09}, priority = {2}, title = {RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data}, url = {http://dx.doi.org/10.1093/bioinformatics/btp459}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:5308811 L3 - citeulike-article-id:5308811 N2 - 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@imb.uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics Online. 10.1093/bioinformatics/btp459 IS - 19 JF - Bioinformatics SN - 1460-2059 EP - 2616 TI - RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data VL - 25 SP - 2615 KW - data KW - high-throughput KW - mapping KW - recursive KW - rna KW - rna-seq KW - sequencing KW - strategy AU - Cloonan, Nicole AU - Xu, Qinying AU - Faulkner, Geoffrey AU - Taylor, Darrin AU - Tang, Dave AU - Kolle, Gabriel AU - Grimmond, Sean PY - 2009/10/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btp459 ER -