| Accession | GMS-64-9 (FID: 449)Browse (ALL) GSM4275421_NB-CTRL-DpnII-1.5000.mcool |
| Title | Smc3 and B-cell transit |
| Submit date | 2023-12-22 17:08:17 |
| Last update date | 2024-01-04 15:48:10 |
| Contact | Sung-Joon PARK park AT hgc.jp The University of Tokyo |
| Sharing | open access |
| Keywords | Hi-C Lymphoma B cell |
| HiC file | GSM4275421_NB-CTRL-DpnII-1.5000 (397.32 MB) hic mCool Cooler-Tree |
| Result file | DomainCall.tar.gz (41.18 MB) |
| Submit date | 2024-01-08 14:58:24 |
| Reference | mm10 (Mouse)
 |
| Domains (4DN) | N/A |
| Region | chr:xxx-yyy |
| Methods | ArrowHead hicCups hicDetectLoops DiamondInsulation |
>java -Xmx16g -jar juicer_tools.jar arrowhead --threads 4 -k KR -m 2000
>java -Xmx16g -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 -Xmx16g -jar juicer_tools.jar apa --threads 4
>hicDetectLoops --threads 4 --peakWidth 2 --windowSize 5 --pValuePreselection 0.1 --peakInteractionsThreshold 10 --obsExpThreshold 1.5 --pValue 0.025 --maxLoopDistance 2000000 --threadsPerChromosome 1 --expected mean
>cooltools diamond-insulation --ignore-diags 2 --append-raw-scores --min-frac-valid-pixels 0.66 --min-dist-bad-bin 0 --chunksize 2000000
