Cargando…

BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

The incorporation of unique molecular identifiers (UMIs) in single-cell RNA-seq assays makes possible the identification of duplicated molecules, thereby facilitating the counting of distinct molecules from sequenced reads. However, we show that the naïve removal of duplicates can lead to a bias due...

Descripción completa

Detalles Bibliográficos
Autores principales:	Gustafsson, Johan, Robinson, Jonathan, Nielsen, Jens, Pachter, Lior
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2021
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8188791/ https://www.ncbi.nlm.nih.gov/pubmed/34103073 http://dx.doi.org/10.1186/s13059-021-02386-z

Ejemplares similares

Improving RNA-Seq expression estimates by correcting for fragment bias
por: Roberts, Adam, et al.
Publicado: (2011)

Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts
por: Ntranos, Vasilis, et al.
Publicado: (2016)

Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers
por: Townes, F. William, et al.
Publicado: (2020)

CGAL: computing genome assembly likelihoods
por: Rahman, Atif, et al.
Publicado: (2013)

MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq
por: Hill, Jonathon T., et al.
Publicado: (2013)

Genotype-free demultiplexing of pooled single-cell RNA-seq
por: Xu, Jun, et al.
Publicado: (2019)

Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference
por: Huang, Yuanhua, et al.
Publicado: (2019)

Gene-level differential analysis at transcript-level resolution
por: Yi, Lynn, et al.
Publicado: (2018)

SWALO: scaffolding with assembly likelihood optimization
por: Rahman, Atif, et al.
Publicado: (2021)

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome
por: Omasits, Ulrich, et al.
Publicado: (2013)

Sources of variation in cell-type RNA-Seq profiles
por: Gustafsson, Johan, et al.
Publicado: (2020)

RNA-Seq and find: entering the RNA deep field
por: Roberts, Adam, et al.
Publicado: (2011)

CRISPR/Cas9 screening using unique molecular identifiers
por: Schmierer, Bernhard, et al.
Publicado: (2017)

Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries
por: Riemondy, Kent A, et al.
Publicado: (2019)

A genome-wide study of preferential amplification/hybridization in microarray-based pooled DNA experiments
por: Yang, H.-C., et al.
Publicado: (2006)

Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells
por: Khan, Arshad H., et al.
Publicado: (2020)

DSAVE: Detection of misclassified cells in single-cell RNA-Seq data
por: Gustafsson, Johan, et al.
Publicado: (2020)

LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis
por: Lyu, Jun, et al.
Publicado: (2023)

Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases
por: Merlin, Christine, et al.
Publicado: (2013)

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data
por: Jia, Wenlong, et al.
Publicado: (2013)

pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens
por: Hundal, Jasreet, et al.
Publicado: (2016)

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments
por: Korthauer, Keegan D., et al.
Publicado: (2016)

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data
por: Cmero, Marek, et al.
Publicado: (2021)

ReSeq simulates realistic Illumina high-throughput sequencing data
por: Schmeing, Stephan, et al.
Publicado: (2021)

SeqOthello: querying RNA-seq experiments at scale
por: Yu, Ye, et al.
Publicado: (2018)

Pooled Sequencing and Rare Variant Association Tests for Identifying the Determinants of Emerging Drug Resistance in Malaria Parasites
por: Cheeseman, Ian H., et al.
Publicado: (2015)

A scaling normalization method for differential expression analysis of RNA-seq data
por: Robinson, Mark D, et al.
Publicado: (2010)

A long-read RNA-seq approach to identify novel transcripts of very large genes
por: Uapinyoying, Prech, et al.
Publicado: (2020)

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
por: Smith, Tom, et al.
Publicado: (2017)

Shape-based peak identification for ChIP-Seq
por: Hower, Valerie, et al.
Publicado: (2011)

TopHat: discovering splice junctions with RNA-Seq
por: Trapnell, Cole, et al.
Publicado: (2009)

An improved method to identify BAC clones using pooled overgos
por: Madishetty, Kavitha, et al.
Publicado: (2007)

In situ genotyping of a pooled strain library after characterizing complex phenotypes
por: Lawson, Michael J, et al.
Publicado: (2017)

Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis
por: Niranjan, Tejasvi S, et al.
Publicado: (2011)

Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives
por: Jeong, Hyun-Hwan, et al.
Publicado: (2019)

Normalization of single-cell RNA-seq counts by log(x + 1)(†) or log(1 + x)(†)
por: Booeshaghi, A Sina, et al.
Publicado: (2021)

EnD-Seq and AppEnD: sequencing 3′ ends to identify nontemplated tails and degradation intermediates
por: Welch, Joshua D., et al.
Publicado: (2015)

Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations
por: Ho, Yu-Jui, et al.
Publicado: (2018)

CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq
por: Hashimshony, Tamar, et al.
Publicado: (2016)

Saturation analysis of ChIP-seq data for reproducible identification of binding peaks
por: Hansen, Peter, et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_p3n5ea0ljjg52foojh6hvc1u4b