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Aberration-corrected ultrafine analysis of miRNA reads at single-base resolution: a k-mer lattice approach

Zhang, Xuan, Ping, Pengyao, Hutvagner, Gyorgy, Blumenstein, Michael, Li, Jinyan·2021·Nucleic Acids Research
DOI 10.1093/nar/gkab610PMC PMC8631080
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Abstract

Raw sequencing reads of miRNAs contain machine-made substitution errors, or even insertions and deletions (indels). Although the error rate can be low at 0.1%, precise rectification of these errors is critically important because isoform variation analysis at single-base resolution such as novel isomiR discovery, editing events understanding, differential expression analysis, or tissue-specific isoform identification is very sensitive to base positions and copy counts of the reads. Existing error correction methods do not work for miRNA sequencing data attributed to miRNAs’ length and per-read-coverage properties distinct from DNA or mRNA sequencing reads. We present a novel lattice structure combining kmers, (k – 1)mers and (k + 1)mers to address this problem. The method is particularly effective for the correction of indel errors. Extensive tests on datasets having known ground truth of errors demonstrate that the method is able to remove almost all of the errors, without introducing any new error, to improve the data quality from every-50-reads containing one error to every-1300-reads containing one error. Studies on experimental miRNA sequencing datasets show that the errors are often rectified at the 5′ ends and the seed regions of the reads, and that there are remarkable changes after the correction in miRNA isoform abundance, volume of singleton reads, overall entropy, isomiR families, tissue-specific miRNAs, and rare-miRNA quantities.

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  • All runs were evaluated for adapter sequences, and any samples with barcodes, unique molecular identifiers (UMIs), or adapter sequences on both ends were not processed (n = 1,870 runs were removed).

    “All runs were evaluated for adapter sequences, and any samples with barcodes, unique molecular identifiers (UMIs), or adapter sequences on both ends were not processed (n = 1,870 runs were removed) due to the use of miREC in the processing [47].”

    From A curated human cellular microRNAome based on 196 primary cell types (2022) · cites this paper as [47]

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Cited by

Sorted by citations

Authors
Zhang, X., Ping, P., Hutvagner, G., Blumenstein, M., & Li, J.
Affiliations
  • Data Science Institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
  • School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
  • Faculty of Engineering and IT, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2021-07-21
Volume
49
Issue
18
Pages
e106-e106
ISSN
  • 0305-1048
  • 1362-4962
DOI
10.1093/nar/gkab610
PMC
PMC8631080
Cited by
11
References
2
Language
en
Licence
creativecommons.org/licenses/by-nc/4.0/ (vor, 1 d)
Funders
Australian Research Council (DP 180100120)

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