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DropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments.

ABSTRACT: Recent single-cell RNA-seq protocols based on droplet microfluidics use massively multiplexed barcoding to enable simultaneous measurements of transcriptomes for thousands of individual cells. The increasing complexity of such data creates challenges for subsequent computational processing and troubleshooting of these experiments, with few software options currently available. Here, we describe a flexible pipeline for processing droplet-based transcriptome data that implements barcode corrections, classification of cell quality, and diagnostic information about the droplet libraries. We introduce advanced methods for correcting composition bias and sequencing errors affecting cellular and molecular barcodes to provide more accurate estimates of molecular counts in individual cells.

SUBMITTER: Petukhov V

PROVIDER: S-EPMC6010209 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments.

Petukhov Viktor V Guo Jimin J Baryawno Ninib N Severe Nicolas N Scadden David T DT Samsonova Maria G MG Kharchenko Peter V PV

Genome biology 20180619 1

Recent single-cell RNA-seq protocols based on droplet microfluidics use massively multiplexed barcoding to enable simultaneous measurements of transcriptomes for thousands of individual cells. The increasing complexity of such data creates challenges for subsequent computational processing and troubleshooting of these experiments, with few software options currently available. Here, we describe a flexible pipeline for processing droplet-based transcriptome data that implements barcode correction ...[more]

PMID: 29921301

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