Information
Accession GMS-65-49 (FID: 496)Browse (ALL)
Title Hi-C on GM12878 cells - protocol variations
HiC file 4DNFIX4PJKXZ (1.60 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 10:06:56
Last update date2025-01-17 10:06:56
Contact GMSuite GENOMEMODALITY
gmsuite AT hgc.jp
The University of Tokyo
Sharingopen access
Keywords Hi-C  4DN  contact matrix 
 Domain/Loop Calling Information

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Submit date 2025-01-17 10:06:57
Reference hg38 (Human)  
Result file DomainCall.tar.gz (214.97 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 843 domains
1650 boundaries
GMS Loop 3290 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (1650)
CTCF(+) RAD21(-)  58 (3.52%)
CTCF(-) RAD21(+)  41 (2.48%)
CTCF(+) RAD21(+)  182 (11.03%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C 66 3.617 0.502
HOXA4 43 3.512 0.519
RBPJ 47 3.499 0.502
CTCF 33 3.136 0.524
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (3290 x2 anchors)
CTCF(+) RAD21(-)  122 (3.71%) LA
 156 (4.74%) RA
 8 (0.24%) LA & RA
CTCF(-) RAD21(+)  87 (2.64%) LA
 85 (2.58%) RA
 4 (0.12%) LA & RA
CTCF(+) RAD21(+)  568 (17.26%) LA
 601 (18.27%) RA
 131 (3.98%) LA + RA
CTCF directionality
(3290 cases)		  111 (3.37%)Convergent ≫ ≪
 9 (0.27%)Divergent ≪ ≫
 64 (1.95%)Tandem ≫ ≫
 1079 (32.8%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox558544.4100.569
MEIS144836.7570.505
RHOXF137936.7400.534
Nr2e337436.3460.508
CTCF24431.6720.560
FOXL136028.2330.529
FOXI134226.4290.529
FOXO434226.4290.528
FOXO634226.4290.526
FOXP334226.2220.521
 CTCF&RAD21 in Loop Anchors
 CTCF directionality
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
 Figures
APA (5K)
 normedAPA (5K)
 centerNormedAPA (5K)
 rankAPA (5K)
APA (10K)
 normedAPA (10K)
 centerNormedAPA (10K)
 rankAPA (10K)
APA (25K)
 normedAPA (25K)
 centerNormedAPA (25K)
 rankAPA (25K)
%>4DN_get_insulation_scores_and_boundaries --bweak 0.2 --bstrong 0.5 --cutoff 2 --pixels_frac 0.66
  "--binsize 5000 --window 100000,--binsize 10000 --window 100000"

%>java -Xmx32g -jar /usr/proj/gmsuite/TOOL/Juicer/scripts/common/juicer_tools.jar arrowhead --ignore-sparsity --threads 4 -k KR -m 2000

%>java -Xmx32g -jar /usr/proj/gmsuite/TOOL/Juicer/scripts/common/juicer_tools.jar hiccups --ignore-sparsity --cpu --threads 4 -k KR -m 1024 -f .1,.1,.1 -p 4,2,1 -i 7,5,3 -t 0.02,1.5,1.75 -d 20000,20000,50000 -r 5000,10000,25000

%>java -Xmx32g -jar /usr/proj/gmsuite/TOOL/Juicer/scripts/common/juicer_tools.jar apa --ignore-sparsity --threads 4

%>hicDetectLoops --threads 2 --peakWidth 2 --windowSize 5 --pValuePreselection 0.1 --peakInteractionsThreshold 10 --obsExpThreshold 1.5 --pValue 0.025 --maxLoopDistance 2000000 --threadsPerChromosome 1 --expected mean

%>cooltools insulation --ignore-diags 2 --append-raw-scores --min-frac-valid-pixels 0.66 --min-dist-bad-bin 0 --chunksize 2000000
  win= 100000

Creating GMS_Domains.bedpe: "hicMergeDomains" with all Strong boundaries of 4DN and "intersectBed" -a all_ArrowHeads -b Strong_boundaries
%>hicMergeDomains --value 5000

Creating GMS_Loops.bedgraph: "hicMergeLoops" of hicCups merged_loops + all_hicDetectLoops -r 25000
%>hicMergeLoops -r 25000

CTCF&RAD21
%>gimme scan -gc -f 0.1 -b -N 1
Boundaries
%>gimme motifs -b genomic -s 0 -f 0.2 -t Homer --known -p JASPAR2020_vertebrates -N 1
Loops
%>gimme motifs -b genomic -s 5000 -f 0.2 -t Homer --known -p JASPAR2020_vertebrates -N 1