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Evaluation of microRNA alignment techniques

Ziemann, Mark, Kaspi, Antony and El-Osta, Assam 2016, Evaluation of microRNA alignment techniques, RNA, vol. 22, no. 8, pp. 1120-1138, doi: 10.1261/rna.055509.115.

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Title Evaluation of microRNA alignment techniques
Author(s) Ziemann, MarkORCID iD for Ziemann, Mark orcid.org/0000-0002-7688-6974
Kaspi, Antony
El-Osta, Assam
Journal name RNA
Volume number 22
Issue number 8
Start page 1120
End page 1138
Total pages 19
Publisher Cold Spring Harbor Laboratory Press
Place of publication Cold Spring Harbor, N.Y.
Publication date 2016-08
ISSN 1469-9001
Keyword(s) small RNA sequencing
microRNA
next-generation sequencing
short-read aligners
gene expression
science & technology
life sciences & biomedicine
biochemistry & molecular biology
Summary 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 and accuracy of 16 short-read mappers and quantify their robustness to mismatches, indels, and nontemplated nucleotide additions. These were explored in the context of a plant genome (Oryza sativa, ∼500 Mbp) and a mammalian genome (Homo sapiens, ∼3.1 Gbp). Analysis of simulated and real smRNA-seq data demonstrates that mapper selection impacts differential expression results and interpretation. These results will inform on best practice for smRNA mapping and enable more accurate smRNA detection and quantification of expression and RNA editing.
Language eng
DOI 10.1261/rna.055509.115
Field of Research 0601 Biochemistry And Cell Biology
HERDC Research category C1.1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2016, Ziemann et al.
Free to Read? Yes
Use Rights Creative Commons Attribution non-commercial licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30113082

Document type: Journal Article
Collections: School of Life and Environmental Sciences
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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.