ArticleFrontiers in genetics2014
On the optimal trimming of high-throughput mRNA sequence data.
Article in Frontiers in genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
100 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Here We Are, But Where Do We Go? A Systematic Review of Crustacean Transcriptomic Studies from 2014-2015.Integrative and comparative biology · 2016Pooled it
- Comparative Transcriptomic Analyses Identify Candidate Genes for Convergent Reproductive Shifts in a Bimodal Viviparous Amphibian.Molecular ecology · 2026Article
- Differential Immune Responses Correlate With Chytridiomycosis Severity in Italian Crested Newts.Molecular ecology · 2026Article
- The strategies and advances of mRNA translation booster.Asian journal of pharmaceutical sciences · 2025Review
- Metagenome and metabolome study on inhaled corticosteroids in asthma patients with side effects.Journal of integrative bioinformatics · 2025Article
- Preservation of milk in liquid nitrogen during sample collection does not affect the RNA quality for RNA-seq analysis.BMC genomics · 2025Article
- Transcriptomic Data Reveal Divergent Paths of Chitinase Evolution Underlying Dietary Convergence in Anteaters and Pangolins.Genome biology and evolution · 2025Article
- Seeing double: two different homospermidine oxidases are involved in pyrrolizidine alkaloid biosynthesis in different organs of comfrey (Symphytum officinale).The Plant journal : for cell and molecular biology · 2024Article
- First neurotranscriptome of adults Tambaquis (Colossoma macropomum) with characterization and differential expression between males and females.Scientific reports · 2024Article
- Transcriptional signature of host shift in the seed beetle Zabrotes subfasciatus.Genetics and molecular biology · 2024Article
- Using metatranscriptomics to better understand the role of microbial nitrogen cycling in coastal sediment benthic flux denitrification efficiency.Environmental microbiology reports · 2023Article
- An updated de novo transcriptome for green ash (Fraxinus pennsylvanica).G3 (Bethesda, Md.) · 2023Article
- Genomic, functional and structural analyses elucidate evolutionary innovation within the sea anemone 8 toxin family.BMC biology · 2023Article
- Transcriptomic analysis provides insight into the mechanism of IKKβ-mediated suppression of HPV18E6-induced cellular abnormalities.G3 (Bethesda, Md.) · 2023Article
- Pooled analysis of frontal lobe transcriptomic data identifies key mitophagy gene changes in Alzheimer's disease brain.Frontiers in aging neuroscience · 2023Article
- Design, execution, and interpretation of plant RNA-seq analyses.Frontiers in plant science · 2023Review
- Temporal progress of gene expression analysis with RNA-Seq data: A review on the relationship between computational methods.Computational and structural biotechnology journal · 2023Review
- Differential expression of epigenetic modifiers in early and late cardiotoxic heart failure reveals DNA methylation as a key regulator of cardiotoxicity.Frontiers in cardiovascular medicine · 2023Article
- Transcriptome profiling of lung immune responses potentially related to acute respiratory distress syndrome in forest musk deer.BMC genomics · 2022Article
- Natural variation in the maternal and zygotic mRNA complements of the early embryo in Drosophila melanogaster.BMC genomics · 2022Article
40 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The widespread and rapid adoption of high-throughput sequencing technologies has afforded researchers the opportunity to gain a deep understanding of genome level processes that underlie evolutionary change, and perhaps more importantly, the links between genotype and phenotype. In particular, researchers interested in functional biology and adaptation have used these technologies to sequence mRNA transcriptomes of specific tissues, which in turn are often compared to other tissues, or other individuals with different phenotypes. While these techniques are extremely powerful, careful attention to data quality is required. In particular, because high-throughput sequencing is more error-prone than traditional Sanger sequencing, quality trimming of sequence reads should be an important step in all data processing pipelines. While several software packages for quality trimming exist, no general guidelines for the specifics of trimming have been developed. Here, using empirically derived sequence data, I provide general recommendations regarding the optimal strength of trimming, specifically in mRNA-Seq studies. Although very aggressive quality trimming is common, this study suggests that a more gentle trimming, specifically of those nucleotides whose Phred score <2 or <5, is optimal for most studies across a wide variety of metrics.
Indexed as
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.