Simulation-based benchmarking of isoform quantification in single-cell RNA-seq View Full Text


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Article Info

DATE

2018-12

AUTHORS

Jennifer Westoby, Marcela Sjöberg Herrera, Anne C. Ferguson-Smith, Martin Hemberg

ABSTRACT

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 from our analysis of real data which shows that genes that express two isoforms in bulk RNA-seq predominantly express one or neither isoform in individual cells. More... »

PAGES

191

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13059-018-1571-5

    DOI

    http://dx.doi.org/10.1186/s13059-018-1571-5

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30404663


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    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s13059-018-1571-5'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s13059-018-1571-5'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13059-018-1571-5'

    RDF/XML is a standard XML format for linked data.

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