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 jferna10@ucsc.edu
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