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.

Methods

Pickrell et al. 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 -http://eqtl.uchicago.edu/Masking/ +https://www.giladlab.uchicago.edu/data/Masking/ (see the -readme file). +readme file).

Credits

Thanks to Joseph Pickrell at the University of Chicago for these data.

References

Pickrell JK, Gaffney DJ, Gilad Y, Pritchard JK. False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. Bioinformatics. 2011 Aug 1;27(15):2144-6. Epub 2011 Jun 19.