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/t2tRepeatMasker.html src/hg/makeDb/trackDb/human/hs1/html/t2tRepeatMasker.html index c88b297f5bc..6da63bbd039 100644 --- src/hg/makeDb/trackDb/human/hs1/html/t2tRepeatMasker.html +++ src/hg/makeDb/trackDb/human/hs1/html/t2tRepeatMasker.html @@ -154,30 +154,54 @@ </tr> </table> </p> <p> A "?" at the end of the "Family" or "Class" (for example, DNA?) signifies that the curator was unsure of the classification. At some point in the future, either the "?" will be removed or the classification will be changed.</p> <h2>Methods</h2> <p> The RepeatMasker (<a href="www.repeatmasker.org">www.repeatmasker.org</a>) tool was used to generate the datasets found on this track hub. </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>, where the track name is <tt>t2tRepeatMasker</tt>.</p> +<p> +For automated analysis, the data may be downloaded from our +<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/t2tRepeatMasker/" target="_blank">download server</a> as a +bigBed file. The file for this track is called <tt>chm13v2.0_rmsk.bb</tt>. Individual regions or the whole +genome annotation can be obtained using our tool <tt>bigBedToBed</tt>, which can be compiled from +the source code or downloaded as a precompiled binary for your system. Instructions for downloading +source code and binaries can be found +<a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>. +The tool can also be used to obtain only features within a given range, for example:</p> +<tt>bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/t2tRepeatMasker/chm13v2.0_rmsk.bb -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>References</h2> <p> Smit AFA, Hubley R, Green P. <em>RepeatMasker Open-3.0</em>. <a href="https://www.repeatmasker.org/" target="_blank"> https://www.repeatmasker.org/</a>. 1996-2010. </p> <p> For the discovery of the additional T2T-CHM13-derived repeats included in this track, as well as the methods (and scripts) for masking the assembly with these T2T-CHM13-derived repeats and previously known repeats: </p> <p> Hoyt SJ, et al. <a href="https://www.science.org/doi/10.1126/science.abk3112" target="_blank">