ArticleBriefings in bioinformatics2023
The hitchhikers' guide to RNA sequencing and functional analysis.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed.
- Metaviromic profiling of mosquito excreta using superhydrophobic collection devices expands the known RNA virome of North America.Microbiology spectrum · 2026Article
- Liver-Directed Cyp2e1 RNA Interference Attenuates Hepatotoxicity Induced by Triptolide, a Bioactive Diterpenoid fromPharmaceuticals (Basel, Switzerland) · 2026Article
- Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities.Nature communications · 2026Article
- Targeting Non-Coding RNAs as a Potential Therapeutic and Delivery Strategy Against Neurodegenerative Diseases.International journal of molecular sciences · 2026Review
- Review
- RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations.GigaScience · 2026Article
- BIOGEN: evidence-grounded multi-agent reasoning framework for transcriptomic interpretation in antimicrobial resistance.Frontiers in bioinformatics · 2026Article
- Advancing human ovarian biology in tandem with clinical care: considerations for collecting ovarian tissue for research after oophorectomy for tissue cryopreservation.Frontiers in endocrinology · 2026Review
- Article
- Point of Care Testing, Rapid Next Generation Sequencing and Artificial Intelligence in Pediatric and Neonatal Healthcare: A Narrative Review.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Systematic evaluation of metatranscriptomic differential gene expressionbioRxiv : the preprint server for biology · 2025Article
- Early control of cochlear viral load limits cochlear inflammation and prevents virus-induced sensorineural hearing loss.Journal of neuroinflammation · 2025Article
- Integrated TWAS, GWAS, and RNAseq results identify candidate genes associated with reproductive traits in cows.Scientific reports · 2025Article
- Reference-Based Gene Expression Analysis Using Galaxy Server.Methods in molecular biology (Clifton, N.J.) · 2025Article
- TrAnnoScope: A Modular Snakemake Pipeline for Full-Length Transcriptome Analysis and Functional Annotation.Genes · 2024Article
- Comparative case study on NAMs: towards enhancing specific target organ toxicity analysis.Archives of toxicology · 2024Article
- Identification and evaluation of candidate COVID-19 critical genes and medicinal drugs related to plasma cells.BMC infectious diseases · 2024Article
- The Role of Biomarkers in HPV-Positive Head and Neck Squamous Cell Carcinoma: Towards Precision Medicine.Diagnostics (Basel, Switzerland) · 2024Review
- Transcriptome Analysis of Compensatory Growth and Meat Quality Alteration after Varied Restricted Feeding Conditions in Beef Cattle.International journal of molecular sciences · 2024Article
- Single-cell analysis of the epitranscriptome: RNA modifications under the microscope.RNA biology · 2024Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
DNA and RNA sequencing technologies have revolutionized biology and biomedical sciences, sequencing full genomes and transcriptomes at very high speeds and reasonably low costs. RNA sequencing (RNA-Seq) enables transcript identification and quantification, but once sequencing has concluded researchers can be easily overwhelmed with questions such as how to go from raw data to differential expression (DE), pathway analysis and interpretation. Several pipelines and procedures have been developed to this effect. Even though there is no unique way to perform RNA-Seq analysis, it usually follows these steps: 1) raw reads quality check, 2) alignment of reads to a reference genome, 3) aligned reads' summarization according to an annotation file, 4) DE analysis and 5) gene set analysis and/or functional enrichment analysis. Each step requires researchers to make decisions, and the wide variety of options and resulting large volumes of data often lead to interpretation challenges. There also seems to be insufficient guidance on how best to obtain relevant information and derive actionable knowledge from transcription experiments. In this paper, we explain RNA-Seq steps in detail and outline differences and similarities of different popular options, as well as advantages and disadvantages. We also discuss non-coding RNA analysis, multi-omics, meta-transcriptomics and the use of artificial intelligence methods complementing the arsenal of tools available to researchers. Lastly, we perform a complete analysis from raw reads to DE and functional enrichment analysis, visually illustrating how results are not absolute truths and how algorithmic decisions can greatly impact results and interpretation.
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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.