![]() All tested mappers provided highly similar results for mapping Illumina reads of two polymorphic Arabidopsis accessions to the reference genome or transcriptome and for the determination of DGE when the same software was used for processing.īwa (Burrows–Wheeler-Alignment) was developed for mapping short DNA sequences against a reference genome and was extended for RNA-Seq data analysis. Interestingly, when the commercial CLC software was used with its own DGE module instead of DESeq2, strongly diverging results were obtained. Using the software DESeq2 to determine differential gene expression (DGE) between plants exposed to 20 ☌ or 4 ☌ from these read counts showed a large pairwise overlap between the mappers. Between 92.4% and 99.5% of all reads were mapped to the reference genome or transcriptome and the raw count distributions obtained from the different mappers were highly correlated. Here, we compared seven computational tools for their ability to map and quantify Illumina single-end reads from the Arabidopsis thaliana accessions Columbia-0 (Col-0) and N14. However, comparative tests of different tools for RNA-Seq read mapping and quantification have been mainly performed on data from animals or humans, which necessarily neglect, for example, the large genetic variability among natural accessions within plant species. RNA-Sequencing (RNA-Seq) has taken a prominent role in the study of transcriptomic reactions of plants to various environmental and genetic perturbations. EARLY RELEASE: Incidence of Monkeypox Among Unvaccinated Persons Compared with Persons Receiving ≥1 JYNNEOS Vaccine Dose - 32 U.S.Quantification of gene expression is crucial to connect genome sequences with phenotypic and physiological data.EARLY RELEASE: Monkeypox Case Investigation - Cook County Jail, Chicago, Illinois, July–August 2022 September 30, 2022.Rat Hepatitis E case reported in Hong Kong October 2, 2022.Rodents can serve as reservoirs for emerging fungal pathogens: Study suggests October 2, 2022.An open-source computational tool for measuring bacterial biofilm morphology and growth kinetics upon one-sided exposure to an antimicrobial source September 27, 2022.Pseudomonas aeruginosa persister cell formation upon antibiotic exposure in planktonic and biofilm state September 27, 2022.Assessing the fitness of a dual-antiviral drug resistant human influenza virus in the ferret model September 28, 2022. ![]() Bacteriophage-antibiotic combination therapy against extensively drug-resistant Pseudomonas aeruginosa infection to allow liver transplantation in a toddler September 29, 2022.Accurate and fast identification of minimally prepared bacteria phenotypes using Raman spectroscopy assisted by machine learning September 30, 2022.A G358S mutation in the Plasmodium falciparum Na+ pump PfATP4 confers clinically-relevant resistance to cipargamin September 30, 2022.Enhanced neutralization potency of an identical HIV neutralizing antibody expressed as different isotypes is achieved through genetically distinct mechanisms October 1, 2022. ![]()
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