2018
DOI: 10.1093/gigascience/giy059
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zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs

Abstract: BackgroundSingle-cell RNA-sequencing (scRNA-seq) experiments typically analyze hundreds or thousands of cells after amplification of the cDNA. The high throughput is made possible by the early introduction of sample-specific bar codes (BCs), and the amplification bias is alleviated by unique molecular identifiers (UMIs). Thus, the ideal analysis pipeline for scRNA-seq data needs to efficiently tabulate reads according to both BC and UMI.Findings zUMIs is a pipeline that can handle both known and random BCs and… Show more

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Cited by 331 publications
(272 citation statements)
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“…We sequenced finished libraries as paired-end reads on an Illumina NextSeq500. Reads were mapped and counted using zUMIs 21 , which uses STAR 22 two-pass mapping and featureCounts through Rsubread to count. For the Delaughter et al and Nomura et al datasets, we mapped reads using the same approach as with data generated in this manuscript.…”
Section: Scrna-seq Library Preparation and Analysismentioning
confidence: 99%
“…We sequenced finished libraries as paired-end reads on an Illumina NextSeq500. Reads were mapped and counted using zUMIs 21 , which uses STAR 22 two-pass mapping and featureCounts through Rsubread to count. For the Delaughter et al and Nomura et al datasets, we mapped reads using the same approach as with data generated in this manuscript.…”
Section: Scrna-seq Library Preparation and Analysismentioning
confidence: 99%
“…Vega (VEGA68) and RefSeq (Release 85) ( Supplementary Table S2). zUMIs is a 313 fast and flexible pipeline for processing scRNA-seq data where cell barcode or UMI reads 314 with low sequence quality reads are filtered out prior to UMI collapsing by sequence 315 identity which yields identical count results as UMI-tools 45,44 . For Smart-Seq2 we 316 use the same pipeline settings as in zUMIs, simply omitting the UMI collapsing step 317…”
mentioning
confidence: 99%
“…The sequenced reads of RNA-seq dataset were processed using zUMIs (version 2.2.1) 808 (Parekh et al 2018) with STAR (version 2.6.1a) (Dobin et al 2013), samtools (version 1.9) (H. 809 Li et al 2009) and featureCounts from Rsubread (version 1.32.4) (Liao, Smyth, and Shi 2014). 810…”
Section: Rna-seq 803mentioning
confidence: 99%