This track shows the coverage track for DNAse I Hypersensitivity sites for cell types from the hg38 DNaseI Hypersensitive Site Master List (125 cell types) from ENCODE/Analysis
Coverage tracks represent the basepair coverage from lifting of hg38 coordinates to the Repeat Browser consensus. Peaks indicate that this region is hypersensitive at most instances of this repeat type across the genome.
Use in combination with the corresponding meta-summit and instance mapping tracks.
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseMasterSites/wgEncodeAwgDnaseMasterSites.bed.gz
gunzip *.gz
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseMasterSites/wgEncodeAwgDnaseMasterSources.tab
awk -v OFS="\t" '{print $1,$2,$3,$8,$5}' wgEncodeAwgDnaseMasterSites.bed > encode_DNAse_5.bed
liftOver -multiple encode_DNAse_5.bed ../lift/hg19_to_hg38reps.over.chain encode_DNAse_5_hg38reps.bed encode_DNAse_5_hg38reps.unmapped
awk -v OFS="\t" '{split($4, a, ","); for(i in a) { if (a[i] ~/^[0-9]+$/ ){print $1,$2,$3,a[i],$5,"+"}}}' encode_DNAse_5_hg38reps.bed | sort -k 4b,4 > encode_DNAse_6_hg38reps.bed
sort -k1b,1 wgEncodeAwgDnaseMasterSources.tab > DNAse_key.tab
join -1 1 -2 4 DNAse_key.tab encode_DNAse_6_hg38reps.bed | awk -v OFS="\t" '{print $3,$4,$5,$2,$6,"+"}' > encode_DNAse_6_hg38reps_named.bed
mv encode_DNAse_6_hg38reps_named.bed ~/hive/jferna10/RepeatBrowserHub/hg38reps/wgEncodeAwgDnaseMasterSites
awk -v OFS="\t" '{print $1,$2,$3,$4,$5,$6 >> "encode_DNAse_6_" $4 ".bed"}' encode_DNAse_6_hg38reps_named.bed
ls *.bed | cut -f 1 -d"."| while read i; do bedSort $i.bed $i.bed ; bedtools genomecov -bg -split -i $i.bed -g ../hg38reps.sizes > temp.bg; bedGraphToBigWig temp.bg ../hg38reps.sizes $i.bw; done
ls *.bed | cut -f 1 -d"."| while read i; do bedToBigBed $i.bed ../hg38reps.sizes $i.bb -type=bed6; done
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