This track shows the mappings data processed from the ENCODE_TFBS_Summits track. 340 factors, 129 cell types.
This track represents the mappings of individual genomic summits to the Repeat Browser. hg38 coordinates populate the name field. Use in combination with the corresponding meta summits and coverage tracks. This composite track has MANY subtracks, please only turn a few on at a time to avoid crashing the browser.
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegDnaseClustered/wgEncodeRegDnaseClusteredV3.bed.gz
gunzip wgEncodeRegDnaseClusteredV3.bed.gz
sed "s/\//-/g" encRegTfbsClusteredWithCells.hg38.bed | awk '{split ($6,a,","); for (i in a) { print ($1"\t"$2"\t"$3"\t"$4"\t"$5"\t+") >> "../hg19/encRegTfbsClustered/encRegTfbsClusteredWithCells_"$4"_"a[i]".bed"}}'
#make bb summits
mkdir ../hg38reps/encRegTfbsClustered
ls ../hg38/encRegTfbsClustered/*.bed | cut -f 4 -d "/" | cut -f 1 -d"." | while read i; do awk '$4=$1":"$2"-"$3' ../hg38/encRegTfbsClustered/*${i}.bed > test.bed; liftOver -multiple test.bed ../lift/hg38_to_hg38reps.over.chain ../hg38reps/encRegTfbsClustered/${i}_hg38reps.bed ../hg38reps/encRegTfbsClustered/${i}_hg38reps.unmapped; bedSort ../hg38reps/encRegTfbsClustered/${i}_hg38reps.bed ../hg38reps/encRegTfbsClustered/${i}_hg38reps.bed; bedToBigBed ../hg38reps/encRegTfbsClustered/${i}_hg38reps.bed ../hg38reps/hg38reps.sizes ../hg38reps/encRegTfbsClustered/${i}_hg38reps.bb; done
#make coverage
ls ../hg38reps/encRegTfbsClustered/*.bed | cut -f 4 -d"/" | cut -f 1 -d"." | while read i; do bedtools genomecov -bg -split -i ../hg38reps/encRegTfbsClustered/${i}.bed -g ../hg38reps/hg38reps.sizes > temp.bg; bedGraphToBigWig temp.bg ../hg38reps/hg38reps.sizes ../hg38reps/encRegTfbsClustered/${i}.bw; done
ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr;9(4):e1001046. PMID: 21526222; PMCID: PMC3079585
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. PMID: 22955616; PMCID: PMC3439153
Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT et al. ENCODE data at the ENCODE portal. Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32. PMID: 26527727; PMC: PMC4702836
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 6;489(7414):91-100. PMID: 22955619
Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012 Sep;22(9):1798-812. PMID: 22955990; PMC: PMC3431495
Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D et al. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 2013 Jan;41(Database issue):D171-6. PMID: 23203885; PMC: PMC3531197
Email max@soe.ucsc.edu or jferna10@ucsc.edu