8bace26a6f90392a326b2d293791e3fc0c5014b0 max Mon Oct 6 16:38:22 2025 -0700 fixing up the splice Ai supertrack html page, refs #35100 diff --git src/hg/makeDb/trackDb/human/spliceImpactSuper.html src/hg/makeDb/trackDb/human/spliceImpactSuper.html index d1fcc0c65e7..19be2d8f869 100644 --- src/hg/makeDb/trackDb/human/spliceImpactSuper.html +++ src/hg/makeDb/trackDb/human/spliceImpactSuper.html @@ -7,47 +7,58 @@ <h3>AbSplice</h3> <p>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. <a target="_blank" href="https://github.com/gagneurlab/absplice/tree/master">AbSplice</a> scores can be computed from VCF files and are based on quantitative tissue-specific splice site annotations (<a target="_blank" href="https://github.com/gagneurlab/splicemap">SpliceMaps</a>). 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 <a target="_blank" href="https://www.gtexportal.org/home/samplingSitePage">Genotype-Tissue Expression (GTEx) dataset</a>. </p> -<h3>SpliceAI</h3> +<h3>SpliceAI Variants</h3> <p>SpliceAI is an <a href="https://github.com/Illumina/SpliceAI" target="_blank">open-source</a> deep learning splicing prediction algorithm that can predict splicing alterations caused by DNA variations. -Such variants may activate nearby cryptic splice sites, leading to abnormal transcript isoforms. +To score variants, the spliceAI algorithm is run on the genome sequence itself and scores each +nucleotide for the probability that it is a donor or acceptor site, on both the +forward and the reverse strand. Then variants are added to the sequence and the new sequence is +scored. Variants may activate nearby cryptic splice sites, leading to abnormal transcript isoforms. SpliceAI was developed at Illumina; a <a href="https://spliceailookup.broadinstitute.org" target="_blank">lookup tool</a> is provided by the Broad institute. </p> + +<h3>SpliceAI Wildtype</h3> +<p>This "wildtype" container track shows the scores for the genome +sequence itself, without variants. The "wildtype" subtracks are +useful when looking at new transcript models, to evaluate how likely exon +boundaries are and where possible splice acceptor sites are, in combination with the variants track. +</p> + <b>Why are some variants not scored by SpliceAI?</b> <p> SpliceAI only annotates variants within genes defined by the gene annotation file. Additionally, SpliceAI does not annotate variants if they are close to chromosome ends (5kb on either side), deletions of length greater than twice the input parameter -D, or inconsistent with the reference fasta file. </p> -<b>What are the differeneces between masked and unmasked tracks?</b> +<b>What are the differences between masked and unmasked tracks?</b> <p> The unmasked tracks include splicing changes corresponding to strengthening annotated splice sites and weakening unannotated splice sites, which are typically much less pathogenic than weakening annotated splice sites and strengthening unannotated splice sites. The delta scores of such splicing changes are set to 0 in the masked files. We recommend using the unmasked tracks for alternative splicing analysis and masked tracks for variant interpretation. </p> <h3>SpliceVarDB</h3> <p>SpliceVarDB is an online database consolidating over 50,000 variants assayed for their effects on splicing in over 8,000 human genes. The authors evaluated over 500 published data sources and established a spliceogenicity scale to standardize, harmonize, and consolidate variant validation data generated by a range of experimental protocols. Genes and variant locations were obtained using GENCODE v44. Splice regions were calculated as specific distances from the closest @@ -156,30 +167,38 @@ <li>Donor loss score</li> <li>Relative location of affected cryptic acceptor</li> <li>Relative location of affected acceptor</li> <li>Relative location of affected cryptic donor</li> <li>Relative location of affected donor</li> </ul> <p> Since most of the values are 0 or almost 0, we selected only those variants with a score equal to or greater than 0.02. </p> <p> The complete processing of this track can be found in the <a target="_blank" href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/spliceAI/spliceAI.py"> makedoc</a>. </p> +<h3>SpliceAI wildtype</h3> +<p>Data was provided by the Michael Hiller lab. +SpliceAI was run on the entire genome reference chromosomes. +Since the algorithm does not know where transcripts start or end, +the scores can differ from other websites, especially for splice sites +before the last exon or around the first exon. +</p> + <h3>SpliceVarDB</h3> <p>The data was converted by Patricia Sullivan from SpliceVarDB to <a href="../../goldenPath/help/bigLolly.html">bigLolly format</a>, and the UCSC Browser staff downloaded it for display. </p> <h2>Data Access</h2> <p>Precomputed AbSplice-DNA scores in all 49 GTEx tissues are available at <a target="_blank" href="https://zenodo.org/search?q=AbSplice-DNA&l=list&p=1&s=10&sort=bestmatch"> Zenodo</a>.</p> <b>License</b> <p>