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 @@ -1,40 +1,40 @@ <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="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> +<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>