7072384d5e6f4228bec4186d3d677527be0c9bc5 mspeir Fri Jun 26 09:37:20 2026 -0700 Adding data access to hs1 pages on the RR, refs # diff --git src/hg/makeDb/trackDb/human/hs1/html/microsatellites.html src/hg/makeDb/trackDb/human/hs1/html/microsatellites.html index 2209b10e97b..35a4236a935 100644 --- src/hg/makeDb/trackDb/human/hs1/html/microsatellites.html +++ src/hg/makeDb/trackDb/human/hs1/html/microsatellites.html @@ -1,31 +1,55 @@ <h2>Description</h2> <p>This track represents % of simple-sequence (2-mer) repeat pattern. Sequences composed of GA/TC/GC/AT bases are counted if one of the bases repeats (e.g. AAAATTTTAAATT are counted as 13 ATs). Patterns are obtained from every non-verlapping 128 bp window. Values displayed are the % of bases forming the specific repeat type, with a maximum value of 100. These sequence patterns are useful for predicting HiFi or ONT coverage biases, as described in Nurk et al. 2022 (Fig. 3) and Mc Cartney et al., 2022. </p> <h2>Display Conventions and Configuration</h2> <!-- if there are special conventions, like colors, describe them here --> <ul> <li><span style='border: 1px inset #000000; background-color:#5369FF;'> </span> - GA <li><span style='border: 1px inset #000000; background-color:#660066;'> </span> - TC <li><span style='border: 1px inset #000000; background-color:#BC7313;'> </span> - GC <li><span style='border: 1px inset #000000; background-color:#336600;'> </span> - AT </ul> <h2>Methods</h2> <p>The track was generated using <a href="https://github.com/marbl/seqrequester">Seqrequester</a>, a Meryl and Canu utility module. The tracks can be generated using <code>seqrequester microsatellite</code>. The code to generate these patterns can be found at <a href="https://github.com/arangrhie/T2T-Polish/tree/master/pattern">T2T-Polish/pattern</a>.</p> +<h2>Data Access</h2> +<p> +The raw data can be explored interactively with the +<a href="../cgi-bin/hgTables" target="_blank">Table Browser</a> or the +<a href="../cgi-bin/hgIntegrator" target="_blank">Data Integrator</a>. The data can also be +accessed from scripts through our <a href="https://api.genome.ucsc.edu" target="_blank">REST +API</a>.</p> +<p> +This track is a container of multiple subtracks; the underlying data are stored in bigWig files +that can be downloaded from our +<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/microsatellites/" target="_blank">download server</a>. +Individual regions or the whole genome annotation can be obtained using our tool +<tt>bigWigToWig</tt>, which can be compiled from the source code or downloaded as a precompiled +binary for your system. Instructions for downloading source code and binaries can be found +<a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>. +The tool can also be used to obtain only features within a given range, for example:</p> +<tt>bigWigToWig https://hgdownload.soe.ucsc.edu/gbdb/$db/microsatellites/chm13v2.0.microsatellite.GA.128.bw -chrom=chr6 -start=0 -end=1000000 stdout</tt> +<p> +Please refer to our +<a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome" target="_blank">mailing +list archives</a> for questions, or our +<a href="../FAQ/FAQdownloads.html#download36" target="_blank">Data Access FAQ</a> for more +information.</p> + <h2>Release history</h2> <ul> <li>2021/05/24, Microsatellite tracks for chm13.v1.0 assembly.</li> <li>2021/10/13, Microsatellite tracks for chm13.v1.1 assembly.</li> <li>2022/03/29, Microsatellite tracks for chm13.v2.0 assembly.</li> </ul> <h2>Credits</h2> <p>For inquiries, please contact us at <a href="https://github.com/marbl/seqrequester">Seqrequester</a> or <a href="https://github.com/arangrhie/T2T-Polish">T2T-Polish</a>.</p> <h2>References</h2> <ol> <li>Nurk S, Koren S, Rhie A, Rautiainen M <em>et al</em>. The complete sequence of a human genome. <em>Science</em> (2022) doi: <a href="https://doi.org/10.1126/science.abj6987">10.1126/science.abj6987</a></li> <li>Mc Cartney AM, Shafin K, Alonge M <em>et al</em>. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. <em>Nat. Methods</em> (2022) doi: <a href="https://doi.org/10.1038/s41592-022-01440-3">10.1038/s41592-022-01440-3</a></li> </p>