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/bamSLDenisova.html src/hg/makeDb/trackDb/human/bamSLDenisova.html
index ef73330..a2f3ab9 100644
--- src/hg/makeDb/trackDb/human/bamSLDenisova.html
+++ src/hg/makeDb/trackDb/human/bamSLDenisova.html
@@ -1,68 +1,68 @@
 <!-- Display image in righthand corner -->
 <TABLE ALIGN=RIGHT BORDER=0 WIDTH=441 HEIGHT=655>
   <TR><TD ALIGN=RIGHT>
     <IMG SRC="../images/denisovaCave.jpg" WIDTH=426 HEIGHT=640
 	ALT="Denisova cave">
   </TD></TR>
   <TR><TD ALIGN=RIGHT>
     <FONT SIZE=-1>Denisova cave entrance in the Altai Mountains
 	of Siberia, Russia where the bones were found from which
 	DNA was sequenced
     </FONT>
     <FONT SIZE=-2> (Copyright (C) 2010, Johannes Krause)
     </FONT>
   </TD></TR>
 </TABLE>
 
 <H2>Description</H2>
 <P>
 The Denisova track shows Denisova sequence reads mapped to the
 $organism genome. The Denisova sequence was generated from a phalanx bone
 excavated from Denisova Cave in the Altai Mountains in southern
 Siberia.
 </P>
 
 <H2>Methods</H2>
 <P>
 Denisova sequence libraries were prepared by treating DNA extracted
 from a single phalanx bone with two enzymes: uracil-DNA-glycosylase,
 which removes uracil residues from DNA to leave abasic sites, and
 endonuclease VIII, which cuts DNA at the 59 and 39 sides of abasic
 sites. Subsequent incubation with T4 polynucleotide kinase and T4 DNA
 polymerase was used to generate phosphorylated blunt ends that are
 amenable to adaptor ligation. Because the great majority of uracil
 residues occur close to the ends of ancient DNA molecules, this
 procedure leads to only a moderate reduction in average length of the
 molecules in the library, but a several-fold reduction in
 uracil-derived nucleotide misincorporation. Reads were aligned
 to $organism sequence $date using the
-<A HREF="http://bio-bwa.sourceforge.net/"
+<A HREF="https://bio-bwa.sourceforge.net/"
 TARGET=_blank>Burrows-Wheeler Aligner.</A>
 </P>
 <P>
 <A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/denisova/">Download</A> the 
 Denisova track data sets from the Genome Browser downloads server.
 </P>
 
 <H2>References</H2>
 <P>
 Briggs A.W., Stenzel U., Meyer M., Krause J., Kircher M., P&#228;&#228;bo S. 
 <A HREF="https://academic.oup.com/nar/article/38/6/e87/3112544"
 TARGET=_blank> Removal of deaminated cytosines and detection of in vivo
 methylation in ancient DNA</A>.
 <EM>Nucleic Acids Res.</EM> 2009 Dec 22:38(6) e87.
 </P>
 <P>
 Reich D., Green R.E., Kircher M., Krause J., Patterson N., Durand E.Y., Viola B., 
 Briggs A.W., Stenzel U., Johnson P.L.F. <EM>et al</EM>.
 <A HREF="https://www.nature.com/articles/nature09710"
 TARGET=_blank>
 Genetic history of an archaic hominin group from Denisova Cave in Siberia</A>.
 <EM>Nature.</EM> 2010 Dec 23;468:1053-1060.
 </P>
 
 <H2>Credits</H2>
 <P>
 This track was produced at UCSC using data generated by the Max Planck
 Institute for Evolutionary Anthropology.
 </P>