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Limitations of alignment-free tools in total RNA-seq quantification.

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  • معلومة اضافية
    • المصدر:
      Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
    • بيانات النشر:
      Original Publication: London : BioMed Central, [2000-
    • الموضوع:
      RNA/*chemistry ; Sequence Analysis, RNA/*methods; Algorithms ; Area Under Curve ; High-Throughput Nucleotide Sequencing ; RNA/metabolism ; RNA, Ribosomal/chemistry ; RNA, Ribosomal/metabolism ; RNA, Transfer/chemistry ; RNA, Transfer/metabolism ; ROC Curve
    • نبذة مختصرة :
      Background: Alignment-free RNA quantification tools have significantly increased the speed of RNA-seq analysis. However, it is unclear whether these state-of-the-art RNA-seq analysis pipelines can quantify small RNAs as accurately as they do with long RNAs in the context of total RNA quantification.
      Result: We comprehensively tested and compared four RNA-seq pipelines for accuracy of gene quantification and fold-change estimation. We used a novel total RNA benchmarking dataset in which small non-coding RNAs are highly represented along with other long RNAs. The four RNA-seq pipelines consisted of two commonly-used alignment-free pipelines and two variants of alignment-based pipelines. We found that all pipelines showed high accuracy for quantifying the expression of long and highly-abundant genes. However, alignment-free pipelines showed systematically poorer performance in quantifying lowly-abundant and small RNAs.
      Conclusion: We have shown that alignment-free and traditional alignment-based quantification methods perform similarly for common gene targets, such as protein-coding genes. However, we have identified a potential pitfall in analyzing and quantifying lowly-expressed genes and small RNAs with alignment-free pipelines, especially when these small RNAs contain biological variations.
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    • Grant Information:
      K99 GM087550 United States GM NIGMS NIH HHS; F1607 Welch Foundation (US); GM37949 National Institutes of Health (US); R01 GM037949 United States GM NIGMS NIH HHS; R01 GM088344 United States GM NIGMS NIH HHS
    • Contributed Indexing:
      Keywords: RNA-seq; TGIRT-seq; k-mer
    • الرقم المعرف:
      0 (RNA, Ribosomal)
      63231-63-0 (RNA)
      9014-25-9 (RNA, Transfer)
    • الموضوع:
      Date Created: 20180705 Date Completed: 20181218 Latest Revision: 20201009
    • الموضوع:
      20240829
    • الرقم المعرف:
      PMC6042521
    • الرقم المعرف:
      10.1186/s12864-018-4869-5
    • الرقم المعرف:
      29969991