Description

This track shows the meta-summits track for DNAse I Hypersensitivity sites for cell types from the hg38 DNaseI Hypersensitive Site Master List (125 cell types) from ENCODE/Analysis

Display Conventions and Configuration

Meta-summits indicate that there are peaks on the coverage track suggesting that this region is hypersensitive at most instances of this repeat type across the genome.

Use in combination with the corresponding coverage and instance mapping tracks.

Methods

Using the Repeat Browser bed files (see "instance mapping tracks") we used macs2 to call peaks with the following settings

macs2 callpeak -f BED -t --keep-dup all --outdir data/macs2/ --nomodel --call-summits --extsize 30 -n

macs2 summits and peaks can be found in data/macs2 if you would like to load custom tracks with less stringently filtered meta summits.

References

DNaseI Hypersensitive Site Master List (125 cell types) from ENCODE/Analysis

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B et al. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82. PMID: 22955617; PMC: PMC3721348

John S, Sabo PJ, Thurman RE, Sung MH, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet. 2011 Mar;43(3):264-8. PMID: 21258342

See also the references and credit sections in the related ENCODE Uniform DnaseI HS, ENCODE UW DnaseI HS and ENCODE Duke DnaseI HS tracks.

Email max@soe.ucsc.edu or markd@ucsc.edu