ArticlemSystems2021
FADU: a Quantification Tool for Prokaryotic Transcriptomic Analyses.
Article in mSystems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 33 citations in OpenAlex.
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- Uniform pre-processing of bacterial single-cell RNA-seq.bioRxiv : the preprint server for biology · 2026Article
- Evolutionary assembly of a unique purple-green photosymbiosis revealed by expanded ciliate diversity.The ISME journal · 2026Article
- Dietary fat disrupts a commensal-host lipid network that promotes metabolic health.Cell metabolism · 2026Article
- Transcriptome-guided discovery of novel plant-associated genes in a rhizosphere Pseudomonas.Microbiome · 2025Article
- Phase variation of Clostridioides difficile colony morphology occurs via modulation of cell division.PLoS pathogens · 2025Article
- Symbionts with eroded genomes adjust gene expression according to host life-stage and environment.EMBO reports · 2025Article
- Calprotectin protectsmSystems · 2025Article
- Seasonal transcriptomic shifts reveal metabolic flexibility of chemosynthetic symbionts in an upwelling region.mSystems · 2025Article
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- Metatranscriptomics reveals gene expression dynamics during an anatoxin-a producing Dolichospermum bloom in a western coastal lake.Chemosphere · 2025Article
- Cancer-specific senescence signature promotes malignant phenotypes and immunotherapy resistance in colorectal cancer.Frontiers in immunology · 2025Article
- Metatranscriptomics provide insights into the role of the symbiont Midichloria mitochondrii in Ixodes ticks.FEMS microbiology ecology · 2024Article
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- DistinctbioRxiv : the preprint server for biology · 2024Article
- DistinctFrontiers in microbiomes · 2024Article
- Identification of key biomarkers and associated pathways of pancreatic cancer using integrated transcriptomic and gene network analysis.Saudi journal of biological sciences · 2023Article
- No Transcriptional Compensation for Extreme Gene Dosage Imbalance in Fragmented Bacterial Endosymbionts of Cicadas.Genome biology and evolution · 2023Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
Abstract
Quantification tools for RNA sequencing (RNA-Seq) analyses are often designed and tested using human transcriptomics data sets, in which full-length transcript sequences are well annotated. For prokaryotic transcriptomics experiments, full-length transcript sequences are seldom known, and coding sequences must instead be used for quantification steps in RNA-Seq analyses. However, operons confound accurate quantification of coding sequences since a single transcript does not necessarily equate to a single gene. Here, we introduce FADU (Feature Aggregate Depth Utility), a quantification tool designed specifically for prokaryotic RNA-Seq analyses. FADU assigns partial count values proportional to the length of the fragment overlapping the target feature. To assess the ability of FADU to quantify genes in prokaryotic transcriptomics analyses, we compared its performance to those of eXpress, featureCounts, HTSeq, kallisto, and Salmon across three paired-end read data sets of (i)
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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.