ArticleCell reports methods2026
Quantifying reference alignment bias in functional genomics analyses.
Article in Cell reports methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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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.
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Who cites it
1 citing paper in PubMed.
- Challenges in the detection and assembly of virus integration structures in human genomes.Frontiers in oncology · 2026Review
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Authors and funding
9 authors.
Funding
Abstract
When aligning next-generation sequencing (NGS) reads to a reference genome, differences between the true genome of the individual under study and the reference result in a biased interpretation of aligned data through systematic errors known as reference alignment bias (RAB). The degree to which RAB impacts functional readouts has not been thoroughly quantified. Leveraging resources from the Human Pangenome Reference Consortium, here we quantify RAB in functional genomics assays. Our results indicate that, on average, 0.2% of the genome is susceptible to bias in RNA sequencing (RNA-seq) studies, 1% in ATAC-seq, and 3% in WGBS when using the human reference hg38. Our study quantifies the effect of RAB on functional assays and highlights the importance of using an adequately representative reference genome.
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Registered trials
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