ArticleiScience2022
Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments.
Article in iScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq nanopore long reads data.NAR genomics and bioinformatics · 2026Article
- Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.Nature methods · 2026Article
- RAD: A Read-structure Agnostic Demultiplexer for Single-Cell Long-Read Sequencing and Analysis.bioRxiv : the preprint server for biology · 2026Article
- Current trends and challenges in deciphering single molecule resolution maps of single cell transcriptomes.Briefings in bioinformatics · 2026Review
- Genetic demultiplexing and transcript start site identification from nanopore sequencing of 10x Genomics multiome libraries.bioRxiv : the preprint server for biology · 2026Article
- Review
- Bioinformatics frameworks for single-cell long-read sequencing: unlocking isoform-level resolution.Briefings in bioinformatics · 2025Review
- MysteryMaster: scraping the bottom of the barrel of barcoded Oxford nanopore reads.BMC bioinformatics · 2025Article
- Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform variability in brain cell types.bioRxiv : the preprint server for biology · 2025Article
- Genomic Insights into Tumorigenesis in Newly Diagnosed Multiple Myeloma.Diagnostics (Basel, Switzerland) · 2025Article
- Advances in long-read single-cell transcriptomics.Human genetics · 2024Review
- Advances in single-cell long-read sequencing technologies.NAR genomics and bioinformatics · 2024Article
- Flexiplex: a versatile demultiplexer and search tool for omics data.Bioinformatics (Oxford, England) · 2024Article
- TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator.Bioinformatics (Oxford, England) · 2024Article
- High-sensitive spatially resolved T cell receptor sequencing with SPTCR-seq.Nature communications · 2023Article
- Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE.Genome biology · 2023Article
- Barcode demultiplexing of nanopore sequencing raw signals by unsupervised machine learning.Frontiers in bioinformatics · 2023Article
- Glioma Stem Cells: Novel Data Obtained by Single-Cell Sequencing.International journal of molecular sciences · 2022Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell RNA sequencing allows for characterizing the gene expression landscape at the cell type level. However, because of its use of short-reads, it is severely limited at detecting full-length features of transcripts such as alternative splicing. New library preparation techniques attempt to extend single-cell sequencing by utilizing both long-reads and short-reads. These techniques split the library material, after it is tagged with cellular barcodes, into two pools: one for short-read sequencing and one for long-read sequencing. However, the challenge of utilizing these techniques is that they require matching the cellular barcodes sequenced by the erroneous long-reads to the cellular barcodes detected by the short-reads. To overcome this challenge, we introduce scTagger, a computational method to match cellular barcodes data from long-reads and short-reads. We tested scTagger against another state-of-the-art tool on both real and simulated datasets, and we demonstrate that scTagger has both significantly better accuracy and time efficiency.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.