2020
DOI: 10.1101/2020.06.21.162891
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ASpli2: Integrative analysis of splicing landscapes through RNA-Seq assays

Abstract: Genome-wide analysis of alternative splicing has been a very active field of research since the early days of NGS (Next generation sequencing) technologies. Since then, ever-growing data availability and the development of increasingly sophisticated analysis methods have uncovered the complexity * Corresponding author 1 Equally contributed as well and non-annotated events, bin-associated signals notably increased recall capabilities at a very competitive performance in terms of precision.The vast majority of p… Show more

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Cited by 7 publications
(4 citation statements)
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“…We labeled these three kinds of bins as exon-bin, intron-bin, or AS-bins, respectively. In addition, AS-bins were further classified as defined by Mancini et al (2019). For our analysis, we discarded bins from monoexonic genes and with mean count values lower than five reads per condition.…”
Section: Methodsmentioning
confidence: 99%
“…We labeled these three kinds of bins as exon-bin, intron-bin, or AS-bins, respectively. In addition, AS-bins were further classified as defined by Mancini et al (2019). For our analysis, we discarded bins from monoexonic genes and with mean count values lower than five reads per condition.…”
Section: Methodsmentioning
confidence: 99%
“…We set a significance threshold of 0.05 or less for the adjusted pvalue using the Benjamini and Hochberg method, and required a minimum fold change of at least 2 for the gene to be considered differentially expressed. Differential splicing analysis was performed with ASpli (v.1.5.1) [54] using the default commands as previously described [106].…”
Section: Transcriptome Analysesmentioning
confidence: 99%
“…Of them, the truncated ACE2 transcript ( dACE2 ) that does not bind the SARS-CoV-2 virus but is associated with an interferon-stimulated gene response in experimental models originates from Exon 1c. The exons were counted using the ASpli package in R [ 24 ]. After correcting for overall gene counts and differences in sequence depth, linear models adjusting for batch were used to analyze differences in exon usage in association with interferon-stimulated gene signature and clinical covariates.…”
Section: Methodsmentioning
confidence: 99%