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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, Gabriel Kolle, Sean M. Grimmond
2009 Computer applications in the biosciences : CABIOS  
Here we present RNA-MATE, a computational pipeline based on a recursive mapping strategy for placing strand specific RNAseq data onto a reference genome.  ...  Mapping of next-generation sequencing data derived from RNA samples (RNAseq) presents different genome mapping challenges than data derived from DNA.  ...  ACKNOWLEDGEMENTS The authors greatly appreciate the advice and sequencing data given to us by Ehsan Nourbakhsh and Brooke Gardiner, and the help with LSF and SGE queues given to us by Xuanzhong Li and  ... 
doi:10.1093/bioinformatics/btp459 pmid:19648138 pmcid:PMC2752615 fatcat:h7swlymdx5dvfk6f3x3p2yyvfq

Global and unbiased detection of splice junctions from RNA-seq data

Adam Ameur, Anna Wetterbom, Lars Feuk, Ulf Gyllensten
2010 Genome Biology  
We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts.  ...  When tested on mouse RNA-seq data, > 31,000 splice events were predicted, of which 88% bridged between two regions separated by ≤100 kb, and 74% connected two exons of the same RefSeq gene.  ...  Acknowledgements We thank Jonathan Mangion, Applied Biosystems UK, for his helpful suggestions regarding the software implementation.  ... 
doi:10.1186/gb-2010-11-3-r34 pmid:20236510 pmcid:PMC2864574 fatcat:4doel6wx2vhfzab56vfetsb2sa

Novel Computational Techniques For Mapping And Classifying Next-Generation Sequencing Data

Karel Břinda, Gregory Kucherov, Valentina Boeva
2016 Zenodo  
The pace at which the throughput of sequencing technologies is increasing surpasses the growth of storage and computer capacities, which creates new computational challenges in NGS data processing.  ...  In this thesis, we present novel computational techniques for read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved.  ...  Part II Dynamic read mapping 37 Introduction High-throughput sequencing technologies (Next-Generation Sequencing, commonly abbreviated NGS) made available terabases of DNA sequence data coming from  ... 
doi:10.5281/zenodo.1045317 fatcat:agbwpocisncwvihn2ij5q3ongq