ArticlePloS one2017
The impact of RNA secondary structure on read start locations on the Illumina sequencing platform.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed.
- Exploring per-base quality scores as a surrogate marker of cell-free DNA fragmentome.Briefings in bioinformatics · 2026Article
- Ribosomal RNA processing undergoes surveillance by the mRNA guard protein Npl3.Cellular and molecular life sciences : CMLS · 2026Article
- Variation of gene ratios in mock communities constructed with purified 16S rRNA during processing.Scientific reports · 2024Article
- Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics.Food and environmental virology · 2024Article
- Article
- Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR.International journal of molecular sciences · 2021Article
- Pathomechanisms and biomarkers in facioscapulohumeral muscular dystrophy: roles of DUX4 and PAX7.EMBO molecular medicine · 2021Review
- Inconsistent Patterns of Microbial Diversity and Composition Between Highly Similar Sequencing Protocols: A Case Study With Reef-Building Corals.Frontiers in microbiology · 2021Article
- Article
- Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea.RNA biology · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
High-throughput sequencing is subject to sequence dependent bias, which must be accounted for if researchers are to make precise measurements and draw accurate conclusions from their data. A widely studied source of bias in sequencing is the GC content bias, in which levels of GC content in a genomic region effect the number of reads produced during sequencing. Although some research has been performed on methods to correct for GC bias, there has been little effort to understand the underlying mechanism. The availability of sequencing protocols that target the specific location of structure in nucleic acid molecules enables us to investigate the underlying molecular origin of observed GC bias in sequencing. By applying a parallel analysis of RNA structure (PARS) protocol to bacterial genomes of varying GC content, we are able to observe the relationship between local RNA secondary structure and sequencing outcome, and to establish RNA secondary structure as the significant contributing factor to observed GC bias.
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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.