ArticleNAR genomics and bioinformatics2021
The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 51 citations in OpenAlex.
- Article
- Darkness Attenuates the Early Transcriptional Response to Phosphate Deficiency in Soybean Roots.International journal of molecular sciences · 2026Article
- Handling biological replicates in long-read RNA sequencing data by joining or not joining.Nature communications · 2026Article
- Transcriptional landscape of direct reprogramming toward the hematopoietic lineage.bioRxiv : the preprint server for biology · 2026Article
- HyDRA: A pipeline for integrating long- and short-read RNAseq data for custom transcriptome assembly.iScience · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Article
- E2-regulated transcriptome complexity revealed by long-read direct RNA sequencing: from isoform discovery to truncated proteins.RNA biology · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Comparison of single-cell long-read and short-read transcriptome sequencing via cDNA molecule matching: quality evaluation of the MAS-ISO-seq approach.NAR genomics and bioinformatics · 2025Article
- MicroRNAs in long COVID: roles, diagnostic biomarker potential and detection.Human genomics · 2025Review
- Identification of reproduction-related genes in the hypothalamus of sheep (Ovis aries) using the nanopore full-length transcriptome sequencing technology.Scientific reports · 2024Article
- Accurate long-read transcript discovery and quantification at single-cell, pseudo-bulk and bulk resolution with Isosceles.Nature communications · 2024Article
- DNMT3B splicing dysregulation mediated by SMCHD1 loss contributes to DUX4 overexpression and FSHD pathogenesis.Science advances · 2024Article
- Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data.Nature communications · 2024Article
- Identification and quantification of small exon-containing isoforms in long-read RNA sequencing data.Nucleic acids research · 2023Article
- Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures.Nature methods · 2023Article
- Merging short and stranded long reads improves transcript assembly.PLoS computational biology · 2023Article
- L-GIREMI uncovers RNA editing sites in long-read RNA-seq.Genome biology · 2023Article
- Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq.Advanced genetics (Hoboken, N.J.) · 2023Review
Corrections and comments
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Authors and funding
13 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Application of Oxford Nanopore Technologies' long-read sequencing platform to transcriptomic analysis is increasing in popularity. However, such analysis can be challenging due to the high sequence error and small library sizes, which decreases quantification accuracy and reduces power for statistical testing. Here, we report the analysis of two nanopore RNA-seq datasets with the goal of obtaining gene- and isoform-level differential expression information. A dataset of synthetic, spliced, spike-in RNAs ('sequins') as well as a mouse neural stem cell dataset from samples with a null mutation of the epigenetic regulator
Identifiers
What OpenQuestion holds
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.