ArticleGenome biology2019
Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Increasing usable reads in RNA-seq protocols.iScience · 2026Article
- A combinatorial domain screening platform reveals epigenetic effector interactions for transcriptional perturbation.Nature communications · 2026Article
- Key Considerations on CITE-Seq for Single-Cell Multiomics.Proteomics · 2025Review
- Improving rigor and reproducibility in chromatin immunoprecipitation assay data analysis workflows with Rocketchip.bioRxiv : the preprint server for biology · 2024Article
- Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation.Nucleic acids research · 2023Article
- Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session [13 October 2022].Nutrients · 2023Article
- CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing.PLoS computational biology · 2023Article
- Optimization of enzymatic fragmentation is crucial to maximize genome coverage: a comparison of library preparation methods for Illumina sequencing.BMC genomics · 2022Article
- Customization of a DADA2-based pipeline for fungal internal transcribed spacer 1 (ITS1) amplicon data sets.JCI insight · 2022Article
- Genome Sequence Variations of Infectious Bronchitis Virus Serotypes From Commercial Chickens in Mexico.Frontiers in veterinary science · 2022Article
- Measurement Biases Distort Cell-Free DNA Fragmentation Profiles and Define the Sensitivity of Metagenomic Cell-Free DNA Sequencing Assays.Clinical chemistry · 2021Article
- An optimized protocol for rapid, sensitive and robust on-bead ChIP-seq from primary cells.STAR protocols · 2021Article
- A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2.BMC genomics · 2020Article
- Minority report: the intestinal mycobiota in systemic infections.Current opinion in microbiology · 2020Review
- Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv.Cell systems · 2020Article
- Deconvolution of nucleic-acid length distributions: a gel electrophoresis analysis tool and applications.Nucleic acids research · 2019Article
- Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification.Genome biology · 2019Article
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Authors and funding
11 authors.
Funding
Abstract
Quantification of DNA sequence tags from engineered constructs such as plasmids, transposons, or other transgenes underlies many functional genomics measurements. Typically, such measurements rely on PCR followed by next-generation sequencing. However, PCR amplification can introduce significant quantitative error. We describe REcount, a novel PCR-free direct counting method. Comparing measurements of defined plasmid pools to droplet digital PCR data demonstrates that REcount is highly accurate and reproducible. We use REcount to provide new insights into clustering biases due to molecule length across different Illumina sequencers and illustrate the impacts on interpretation of next-generation sequencing data and the economics of data generation.
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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.