ArticleNucleic acids research2010
Biases in Illumina transcriptome sequencing caused by random hexamer priming.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 390 papers.
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Who cites it
390 citing papers in PubMed.
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- Integrated metabolome and transcriptome analyses reveal the response mechanism under drought stress ofFrontiers in plant science · 2026Article
- Designing RNA sequencing experiments: A practical guide to reproducible gene expression analysis.Computational and structural biotechnology journal · 2026Review
- PeakPrime: a peak-guided primer design pipeline for target enrichment in 3'-end RNA-seq.Bioinformatics advances · 2026Article
- The venom gland transcriptome of Tityus paraguayensis reveals a diverse array of bioactive molecules from the Brazilian Cerrado.PloS one · 2026Article
- Machine Learning Models for Cancer Research: A Narrative Review of Bulk RNA-Seq Applications.International journal of molecular sciences · 2025Review
- A duplex sequencing approach for high-sensitivity detection of genome-edited plants.Food chemistry. Molecular sciences · 2025Article
- New insights into the phylogenetic and biogeographic analysis of Elaeocarpus (Elaeocarpaceae) in China, and further consolidated 'Acronodia' as a distinct group.BMC plant biology · 2025Article
- Deep structural clustering reveals hidden systematic biases in RNA sequencing data.Genome research · 2025Article
- Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner.Genome biology · 2025Article
- GCfix: a fast and accurate fragment length-specific method for correcting GC bias in cell-free DNA.Bioinformatics (Oxford, England) · 2025Article
- Preservation of milk in liquid nitrogen during sample collection does not affect the RNA quality for RNA-seq analysis.BMC genomics · 2025Article
330 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Generation of cDNA using random hexamer priming induces biases in the nucleotide composition at the beginning of transcriptome sequencing reads from the Illumina Genome Analyzer. The bias is independent of organism and laboratory and impacts the uniformity of the reads along the transcriptome. We provide a read count reweighting scheme, based on the nucleotide frequencies of the reads, that mitigates the impact of the bias.
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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.