Alevin efficiently estimates accurate gene abundances from dscRNA-seq data.
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ABSTRACT:
SUBMITTER: Srivastava A
PROVIDER: S-EPMC6437997 | biostudies-literature | 2019 Mar
REPOSITORIES: biostudies-literature
Publications
Alevin efficiently estimates accurate gene abundances from dscRNA-seq data.
Srivastava Avi A Malik Laraib L Smith Tom T Sudbery Ian I Patro Rob R
Genome biology 20190327 1
We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barcode whitelisting. Alevin's approach to UMI deduplication considers transcript-level constraints on the molecules from which UMIs may have arisen and accounts for both gene-unique reads and reads that multimap between genes. This addresses the inherent bias in ...[more]
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