Journal article
Evaluation of microRNA alignment techniques
Mark Ziemann, Antony Kaspi, Assam El-Osta
RNA | COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT | Published : 2016
Abstract
Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses considerable challenges due to their short length (∼21 nucleotides [nt]) as well as the large size and complexity of plant and animal genomes. While several tools have been developed for high-throughput mapping of longer mRNA-seq reads (>30 nt), there are few that are specifically designed for mapping of smRNA reads including microRNAs. The accuracy of these mappers has not been systematically determined in the case of smRNA-seq. In addition, it is unknown whether these aligners accurately map smRNA reads containing sequence errors and polymorphisms. By using simulated read sets, we determine the alignment sensitivity a..
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Funding Acknowledgements
We thank R. Lazarus for bioinformatics support. The authors acknowledge funding support from the Juvenile Diabetes Research Foundation International (JDRF), the National Health and Medical Research Council (NHMRC), and the National Heart Foundation of Australia (NHF). A.E-O. is a Senior Research Fellow supported by the NHMRC. This work was supported in part by the Victorian Government's Operational Infrastructure Support Program.