dc5d2fedb09bf9a1ea4ea9d9348f5cbfe7a21a82
jeltje.van.baren
  Wed Apr 23 11:08:39 2025 -0700
fix typos in recount3.html

diff --git src/hg/makeDb/trackDb/recount3.html src/hg/makeDb/trackDb/recount3.html
index 1dfccbf8870..481ad806789 100644
--- src/hg/makeDb/trackDb/recount3.html
+++ src/hg/makeDb/trackDb/recount3.html
@@ -1,81 +1,81 @@
 <!DOCTYPE html>
 <html>
 <head>
 </head>
 
 <body>
 <h2>Description</h2>
 <p>
 Recount3 is a comprehensive resource for re-analyzing RNA-seq data. It provides uniformly processed 
 RNA-seq data and associated metadata from a wide range of studies, enabling researchers to access 
 and analyze gene expression data in a consistent manner. Recount3 aggregates data from multiple 
 sources, including the Sequence Read Archive (SRA) and the Genotype-Tissue Expression (GTEx) project, 
 and reprocesses it using a standardized pipeline. This allows for cross-study comparisons and 
 meta-analyses, facilitating discoveries in genomics and transcriptomics.
 </p><p>
 These tracks display the recount3 intron data including split read counts.
 </p>
 
 
 <h2>Display Conventions</h2>
 <p>
 Intron blocks are grayscale colored based on read support (darker tones indicate higher coverage). <br>
 Split read counts and splice motifs are shown on mouseover. <br>
 By default only introns with a minimum read count of 10,000 are shown. This setting can be changed
 on the track configuration page. <br>
 The intron ends are color coded: 
 <ul>
 <li><b><font color="#2E2585">Dark blue</font></b> GT donors and AG acceptors (CT and AC on 
 the minus strand) </li>
 <li><b><font color="#5DA899">Teal</font></b> GC donors (GT on the minus strand) </li>
 <li><b><font color="#C26A77">Faded red</font></b> AT donors and AC acceptors (GT and GT on the 
 minus strand) </li>
 </ul>
 Introns with non standard ends do not have colored tags.
 <br>
 The SRA track is only visible when zoomed in within 10 million bases because of its data density.
 </p>
 
 <h2>Data Access</h2>
 The raw data can be explored interactively with the
 <a href="https://genome.ucsc.edu/cgi-bin/hgTables">Table Browser</a> or the
 <a href="https://genome.ucsc.edu/cgi-bin/hgIntegrator">Data Integrator</a>.
 For automated analysis, the data may be queried from our
 <a href="https://genome.ucsc.edu/goldenPath/help/api.html">REST API</a>.<br>
 Please refer to our
 <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">mailing list archives</a>
 for questions, or our
 <a href="https://genome.ucsc.edu/FAQ/FAQdownloads.html#downloads36">Data Access FAQ</a>
 for more information.
 <p>
 The original junction files can be found at <br>
-<a href="https://snaptron.cs.jhu.edu/data/gtexv2/junctions.tgz" target="_blank">
-https://snaptron.cs.jhu.edu/data/gtexv2/junctions.tgz</a><br>
-<a href="https://snaptron.cs.jhu.edu/data/tcgav2/junctions.tgz" target="_blank">
-https://snaptron.cs.jhu.edu/data/tcgav2/junctions.tgz</a><br>
-<a href="https://snaptron.cs.jhu.edu/data/srav3h/junctions.tgz" target="_blank">
-https://snaptron.cs.jhu.edu/data/srav3h/junctions.tgz</a><br>
-<a href="https://snaptron.cs.jhu.edu/data/ccle/junctions.tgz" target="_blank">
-https://snaptron.cs.jhu.edu/data/ccle/junctions.tgz</a><br>
-<a href="https://snaptron.cs.jhu.edu/data/srav1m/junctions.tgz" target="_blank">
-https://snaptron.cs.jhu.edu/data/srav1m/junctions.tgz (mouse)</a><br>
+<a href="https://snaptron.cs.jhu.edu/data/gtexv2/junctions.bgz" target="_blank">
+https://snaptron.cs.jhu.edu/data/gtexv2/junctions.bgz</a><br>
+<a href="https://snaptron.cs.jhu.edu/data/tcgav2/junctions.bgz" target="_blank">
+https://snaptron.cs.jhu.edu/data/tcgav2/junctions.bgz</a><br>
+<a href="https://snaptron.cs.jhu.edu/data/srav3h/junctions.bgz" target="_blank">
+https://snaptron.cs.jhu.edu/data/srav3h/junctions.bgz</a><br>
+<a href="https://snaptron.cs.jhu.edu/data/ccle/junctions.bgz" target="_blank">
+https://snaptron.cs.jhu.edu/data/ccle/junctions.bgz</a><br>
+<a href="https://snaptron.cs.jhu.edu/data/srav1m/junctions.bgz" target="_blank">
+https://snaptron.cs.jhu.edu/data/srav1m/junctions.bgz (mouse)</a><br>
 </p>
 
 <h2>Methods</h2>
 <p>
 Junction files were converted to bed format. For grayscaling total read count was log10
 transformed and multiplied by 10 to get a score between 0 and 225, which can be found
 in the bed score field.
 </p>
 
 <h2>References</h2>
 <p>
 Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT
 <em>et al</em>.
 <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02533-6"
 target="_blank">
 recount3: summaries and queries for large-scale RNA-seq expression and splicing</a>.
 <em>Genome Biol</em>. 2021 Nov 29;22(1):323.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34844637" target="_blank">34844637</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8628444/" target="_blank">PMC8628444</a>
 </p>