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Regions of Exceptionally High Depth of Aligned Short Reads   (All Mapping and Sequencing tracks)

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Description

This track displays regions of the reference genome that have exceptionally high sequence depth, inferred from alignments of short-read sequences from the 1000 Genomes Project. 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.

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/ (see the 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.