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/censat.html src/hg/makeDb/trackDb/human/hs1/html/censat.html index 53bdc97ab6e..b4d33522f20 100644 --- src/hg/makeDb/trackDb/human/hs1/html/censat.html +++ src/hg/makeDb/trackDb/human/hs1/html/censat.html @@ -1,57 +1,81 @@ <h2>Description</h2> <p>Centromeric and Pericentromeric Satellite Annotation (cenSat)</p> <h2>Methods</h2> <p> Satellite array annotations are defined by intersecting information across alpha HOR annotation track, repeatmasker tracks, and human satellite annotation tracks. The broad definition of "peri/centromeric regions" on each chromosome includes the satellite-rich regions and 5 Mb of sequence on the p-arm and q-arm. Although the distal ends of acrocentric short arms are not truly pericentromeric, the vast majority of satellite DNAs present in these arms are highly enriched in peri/centromeric regions on other chromosomes (e.g. HSat1-3, Beta satellites (βSat), Alpha satellites (αSat)). Therefore, acrocentric short arms are included in the cenSat annotation track in their entirety. The Y chromosome peri/centromeric region includes 5 Mb to either side of the active αSat Higher Order Repeat (HOR) array, but we have included satellite array annotations across the entire chromosome. NB: Satellite array annotations typically merge across inserted transposons.</p> <p> Strand information is not included (all annotations are set to + strand)</p> <h2>Display Conventions and Configuration</h2> <!-- if there are special conventions, like colors, describe them here --> <p>Colors</p> <table> <tr><td> <tr><td>Active αSat HOR (hor ... L) <td style="color: #FA0000">red</tr> <tr><td>Inactive αSat HOR (hor) <td style="color: #FF9200">orange</tr> <tr><td>Divergent αSat HOR (dhor) <td style="color: #990000">dark red</tr> <tr><td>Monomeric αSat (mon) <td style="color: #FFCC99">peach/yellow</tr> <tr><td>Classical Human Satellite 1A (hsat1A) <td style="color: #91FF00">light green</tr> <tr><td>Classical Human Satellite 1B (hsat1B) <td style="color: #00994C">dark green</tr> <tr><td>Classical Human Satellite 2 (hsat2) <td style="color: #0080FA">light blue</tr> <tr><td>Classical Human Satellite 3 (hsat3) <td style="color: #0000FA">blue</tr> <tr><td>Beta Satellite (bsat) <td style="color: #FA99FF">pink</tr> <tr><td>Gamma Satellite (gsat) <td style="color: #AC33C7">purple</tr> <tr><td>Other centromeric satellites (censat) <td style="color: #00CCCC">teal</tr> <tr><td>Centromeric transition regions (ct) <td style="color: #E0E0E0">grey</tr> </table> +<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>censat</tt>.</p> +<p> +For automated analysis, the data may be downloaded from our +<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/censat/" target="_blank">download server</a> as a +bigBed file. The file for this track is called <tt>censat.bb</tt>. Individual regions or the whole +genome annotation can be obtained using our tool <tt>bigBedToBed</tt>, which can be compiled from +the source code or downloaded as a precompiled binary for your system. Instructions for downloading +source code and binaries can be found +<a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>. +The tool can also be used to obtain only features within a given range, for example:</p> +<tt>bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/censat/censat.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>Credits</h2> <p> <A HREF="mailto:khmiga@ucsc. edu">Karen Miga <khmiga@ucsc.edu></A>, Nicolas Altemose, Ivan A. Alexandrov </p> <h2>References</h2> <p> Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ <em>et al</em>. <a href="https://www.science.org/doi/10.1126/science.abl4178" target="_blank"> Complete genomic and epigenetic maps of human centromeres</a>. <em>Science</em>. 2022 Apr;376(6588):eabl4178. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35357911" target="_blank">35357911</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9233505/" target="_blank">PMC9233505</a> </p>