f4a0cd933ac7de57b77e8376123c4a14e594152a gperez2 Thu Feb 6 17:02:05 2025 -0800 Updating the SpliceVarDB methods section, refs #34424 diff --git src/hg/makeDb/trackDb/human/spliceImpactSuper.html src/hg/makeDb/trackDb/human/spliceImpactSuper.html index 242e7284c6b..902365f176d 100644 --- src/hg/makeDb/trackDb/human/spliceImpactSuper.html +++ src/hg/makeDb/trackDb/human/spliceImpactSuper.html @@ -63,30 +63,32 @@ can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/splicevardb/" target="_blank">our download server</a>. The file for this track is called <tt>SVADB.bb</tt>. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain only features within a given range, e.g. <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/splicevardb/SVADB.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt></p> </p> </p> <h2>Methods</h2> -<p>The data was converted by Patricia Sullivan from SpliceVarDb within a few -hours to bigLolly format and the UCSC Browser staff needed nothing else to do but to downloaded the data. </p> +<p> +The data was converted by Patricia Sullivan from SpliceVarDB to bigLolly format, and the UCSC +Browser staff downloaded it for display. +</p> <h2>Credits</h2> <p>Thanks to the SpliceVarDB team for converting the data into our data formats.</p> <h2>References</h2> <p> Sullivan PJ, Quinn JMW, Wu W, Pinese M, Cowley MJ. <a href="https://linkinghub.elsevier.com/retrieve/pii/S0002-9297(24)00288-X" target="_blank"> SpliceVarDB: A comprehensive database of experimentally validated human splicing variants</a>. <em>Am J Hum Genet</em>. 2024 Oct 3;111(10):2164-2175. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39226898" target="_blank">39226898</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480807/" target="_blank">PMC11480807</a> </p>