7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3
jnavarr5
  Mon Oct 7 10:55:15 2019 -0700
Updating http to https for hg19, uiLinks cronjob.

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 <H1>Description</H1>
 <P>
 This track displays regions of the reference genome that have exceptionally high
 sequence depth, inferred from alignments of short-read sequences from the
-<A HREF="http://www.internationalgenome.org/" TARGET="_blank">1000 Genomes Project</A>.
+<A HREF="https://www.internationalgenome.org/" TARGET="_blank">1000 Genomes Project</A>.
 These regions may be caused by collapsed repetitive sequences
 in the reference genome assembly; they also have high read depth in assays such as
 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>
 (see the
 <A HREF="http://eqtl.uchicago.edu/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>