| Accession | GMS-65-1 (FID: 228)Browse (ALL) mESC1.intra.hic |
| Title | Intra-chromosomal Hi-C contacts (mESC Rep1) |
| Submit date | 2022-01-31 12:21:48 |
| Last update date | 2024-11-14 15:47:16 |
| Contact | GMSuite GENOMEMODALITY gmsuite AT hgc.jp The University of Tokyo |
| Sharing | open access |
| Keywords | Chromatin PHi-C Hi-C |
| HiC file | mESC1.intra (1.69 GB) hic mCool Cooler-Tree |
| Result file | DomainCall.tar.gz (51.55 MB) |
| Submit date | 2024-11-13 14:31:02 |
| Reference | mm10 (Mouse)
 |
| Domains (4DN) | 10000bin_100000win.bw 5000bin_100000win.bw |
| Region | chr:xxx-yyy |
| Methods | DomainCall_4DN ArrowHead hicCups hicDetectLoops DiamondInsulation |
>4DN_get_insulation_scores_and_boundaries --bweak 0.2 --bstrong 0.5 --cutoff 2 --pixels_frac 0.66
>java -Xmx32g -jar juicer_tools.jar arrowhead --threads 4 -k KR -m 2000
>java -Xmx32g -jar juicer_tools.jar hiccups --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 juicer_tools.jar apa --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
