8c2f7318d8d821de9b2a25750586a94ab5e8c1bb
lrnassar
  Fri Nov 15 18:50:19 2024 -0800
Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM.

diff --git src/hg/makeDb/trackDb/human/hiSeqDepth.html src/hg/makeDb/trackDb/human/hiSeqDepth.html
index c9f1f2b..325e383 100644
--- src/hg/makeDb/trackDb/human/hiSeqDepth.html
+++ src/hg/makeDb/trackDb/human/hiSeqDepth.html
@@ -8,33 +8,33 @@
 ChIP-seq, and may trigger false positive calls from peak-calling algorithms.
 Excluding these regions from analysis of short-read alignments should reduce
 such false positive calls.
 </P>
 
 <H1>Methods</H1>
 <P>
 Pickrell <em>et al.</em> downloaded sequencing reads for 57 Yoruba individuals
 from the 1000 Genomes Project's low-coverage pilot data, mapped them to the
 Mar. 2006 human genome assembly (NCBI36/hg18), computed the read depth for
 every base in the genome, and compiled a distribution of read depths.
 They then identified contiguous regions where read depth exceeded thresholds
 corresponding to the top 0.001, 0.005, 0.01, 0.05 and 0.1 of the per-base 
 read depths, merging regions which fall within 50 bases of each other.
 The regions are available for download from
-<A HREF="http://eqtl.uchicago.edu/Masking/" TARGET="_blank">http://eqtl.uchicago.edu/Masking/</A>
+<A HREF="https://www.giladlab.uchicago.edu/data/Masking/" TARGET="_blank">https://www.giladlab.uchicago.edu/data/Masking/</A>
 (see the
-<A HREF="http://eqtl.uchicago.edu/Masking/readme" TARGET="_blank">readme</A> file).
+<A HREF="https://www.giladlab.uchicago.edu/data/Masking/readme" TARGET="_blank">readme</A> file).
 </P>
 
 <H1>Credits</H1>
 <P>
 Thanks to Joseph Pickrell at the University of Chicago for these data.
 </P>
 
 <H1>References</H1>
 <P>
 Pickrell JK, Gaffney DJ, Gilad Y, Pritchard JK.
 <A HREF="https://academic.oup.com/bioinformatics/article/27/15/2144/404749" TARGET="_blank">
 False positive peaks in ChIP-seq and other sequencing-based
 functional assays caused by unannotated high copy number regions</A>.
 <em>Bioinformatics</em>. 2011 Aug 1;27(15):2144-6. Epub 2011 Jun 19.
 </P>