+AbSplice is a method that predicts aberrant splicing across human tissues, as described in Wagner, +Çelik et al., 2023. This track displays precomputed AbSplice scores for all possible +single-nucleotide variants genome-wide. The scores represent the probability that a given variant +causes aberrant splicing in a given tissue. +AbSplice scores +can be computed from VCF files and are based on quantitative tissue-specific splice site annotations +(SpliceMaps). +While SpliceMaps can be generated for any tissue of interest from a cohort of RNA-seq samples, this +track includes 49 tissues available from the +Genotype-Tissue +Expression (GTEx) dataset. +
+ ++The AbSplice score is a probability estimate of how likely aberrant splicing of some sort takes +place in a given tissue. The authors suggest three cutoffs which are represented by color in the track. +
+ ++Mouseover on items shows the gene name, maximum score, and tissues that had this score. Clicking on +any item brings up a table with scores for all 49 GTEX tissues. +
+ ++The raw data can be explored interactively with the +Table Browser, or the +Data Integrator. +For automated analysis, the data may be queried from our +REST API. +Please refer to our +mailing list archives +for questions, or our +Data Access FAQ +for more information. +
Precomputed AbSplice-DNA scores in all 49 GTEx tissues are available at + +Zenodo. + +
+Data was converted from the files (AbSplice_DNA_ $db _snvs_high_scores.zip) provided by the authors +at zenodo.org. Files in the +score_cutoff=0.01 directory were concatenated. To convert the data to bigBed format, scores and +their tissues were selected from the AbSplice_DNA fields and maximum scores, and then calculated +using a custom Python script, which can be found in the + +makeDoc from our GitHub repository.
+ ++Thanks to Nils Wagner for helpful comments and suggestions.
+ ++Wagner N, Çelik MH, Hölzlwimmer FR, Mertes C, Prokisch H, Yépez VA, Gagneur J. + +Aberrant splicing prediction across human tissues. +Nat Genet. 2023 May;55(5):861-870. +PMID: 37142848 +