+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.
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+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 48 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. +
AbSplice scores are also available at the +public repository created by the authors. +
+ ++Data was converted from the files (AbSplice_DNA_hg38_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 calculated using +a custom +script. +
+ ++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 +