Evaluation of microRNA alignment techniques

Mark Ziemann, Antony Kaspi, Assam El-Osta

Research output: Contribution to journalArticleResearchpeer-review

31 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)1120-1138
Number of pages19
JournalRna-A Publication of the Rna Society
Issue number8
Publication statusPublished - 1 Aug 2016
Externally publishedYes


  • Gene expression
  • MicroRNA
  • Next-generation sequencing
  • Short-read aligners
  • Small RNA sequencing

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