| Accession | GMS-65-109 (FID: 561)Browse (ALL) |
| Title | Hi-C on sync. HeLa cells - Rep3 |
| HiC file | 4DNFIYLJ3R3B (1.25 GB) hic mCool Cooler-Tree |
| Submit date | 2025-01-18 16:30:47 |
| Last update date | 2025-01-18 16:30:47 |
| Contact | GMSuite GENOMEMODALITY gmsuite AT hgc.jp The University of Tokyo |
| Sharing | open access |
| Keywords | Hi-C 4DN contact matrix |
| Submit date | 2025-01-18 16:30:47 |
| Reference | hg38 (Human)
 |
| Result file | DomainCall.tar.gz (167.51 MB) |
| Insulation Score (4DN) | 10000bin_100000win_chrAdded.bw 5000bin_100000win_chrAdded.bw |
| GMS Domain | 29 domains 58 boundaries |
| GMS Loop | 137 loops |
| Hi-C map is too sparse | |
| CTCF(+) RAD21(-) | 2 (3.45%) | ||||||||
| CTCF(-) RAD21(+) | 2 (3.45%) | ||||||||
| CTCF(+) RAD21(+) | 5 (8.62%) | ||||||||
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GimmeMotifs (Pvalue < 0.001, Top10) |
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CTCF&RAD21 in Boundaries Raw ROC file Enriched_motifs.html All_motifs.html |
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| CTCF(+) RAD21(-) | 1 (0.73%) LA 5 (3.65%) RA 0 (0%) LA & RA |
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| CTCF(-) RAD21(+) | 2 (1.46%) LA 3 (2.19%) RA 0 (0%) LA & RA |
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| CTCF(+) RAD21(+) | 16 (11.68%) LA 14 (10.22%) RA 0 (0%) LA + RA |
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| CTCF directionality (137 cases) |
0 (0%)Convergent ≫ ≪ 1 (0.73%)Divergent ≪ ≫ 0 (0%)Tandem ≫ ≫ 34 (24.82%)Singleton ≫ |
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GimmeMotifs (Pvalue < 0.001, Top10) LA+RA |
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CTCF&RAD21 in Loop Anchors CTCF directionality Raw ROC file Enriched_motifs.html All_motifs.html |
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%>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
