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

ABSTRACT: 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.

SUBMITTER: Wu DC

PROVIDER: S-EPMC6042521 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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

Wu Douglas C DC Yao Jun J Ho Kevin S KS Lambowitz Alan M AM Wilke Claus O CO

BMC genomics 20180703 1

<h4>Background</h4>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.<h4>Result</h4>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 wh ...[more]

PMID: 29969991

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Dataset Information

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

Publications

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

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