Simulation-based benchmarking of isoform quantification in single-cell RNA-seq.
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ABSTRACT:
SUBMITTER: Westoby J
PROVIDER: S-EPMC6223048 | biostudies-literature | 2018 Nov
REPOSITORIES: biostudies-literature
Publications
Simulation-based benchmarking of isoform quantification in single-cell RNA-seq.
Westoby Jennifer J Herrera Marcela Sjöberg MS Ferguson-Smith Anne C AC Hemberg Martin M
Genome biology 20181107 1
Single-cell RNA-seq has the potential to facilitate isoform quantification as the confounding factor of a mixed population of cells is eliminated. However, best practice for using existing quantification methods has not been established. We carry out a benchmark for five popular isoform quantification tools. Performance is generally good for simulated data based on SMARTer and SMART-seq2 data. The reduction in performance compared with bulk RNA-seq is small. An important biological insight comes ...[more]
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Project description:BackgroundFull-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA transcripts are long, while RNA-Seq reads are short.ResultsHere we use simulated benchmarking data that reflects many properties of real data, including polymorphisms, intron signal and non-uniform coverage, allowing for systematic comparative analyses of isoform quantification accuracy and its impact on differential expression analysis. Genome, transcriptome and pseudo alignment-based methods are included; and a simple approach is included as a baseline control.ConclusionsSalmon, kallisto, RSEM, and Cufflinks exhibit the highest accuracy on idealized data, while on more realistic data they do not perform dramatically better than the simple approach. We determine the structural parameters with the greatest impact on quantification accuracy to be length and sequence compression complexity and not so much the number of isoforms. The effect of incomplete annotation on performance is also investigated. Overall, the tested methods show sufficient divergence from the truth to suggest that full-length isoform quantification and isoform level DE should still be employed selectively.
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