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4dn:phase2:working_groups:jawg_sandbox
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4dn:phase2:working_groups:jawg_sandbox [2020/05/20 19:47] asli_yildiri |
4dn:phase2:working_groups:jawg_sandbox [2025/04/22 16:21] (current) |
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| ====== Joint Analysis: Data analysis sandbox, with links to analysis products ====== | ====== Joint Analysis: Data analysis sandbox, with links to analysis products ====== | ||
| - | ====== 3D genome mapping method ====== | ||
| ====== Nuclear organization ====== | ====== Nuclear organization ====== | ||
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| ===== Analysis of 3D genome structure population (Alber) ===== | ===== Analysis of 3D genome structure population (Alber) ===== | ||
| - | Using our population-based genome structure modeling protocol described [[https://www.nature.com/articles/nprot.2018.008|here]], we generated populations of 3D genome structures for H1 and HFF (10,000 models each) at 200-kb resolution using Hi-C data available on the 4DN data portal (H1: [[https://data.4dnucleome.org/experiment-set-replicates/4DNES2M5JIGV/|4DNES2M5JIGV]], HFF: [[https://data.4dnucleome.org/experiment-set-replicates/4DNES2R6PUEK/|4DNES2R6PUEK]]). We then calculated the average radial positions of each 200-kb region in the genome across the population (see below). The radial positions range between 0 and 1; 0 means the region is at the center of the nucleus whereas 1 means the region is at the nuclear envelope. | + | Using our population-based genome structure modeling protocol described [[https://www.nature.com/articles/nprot.2018.008|here]], we generated populations of 3D genome structures for H1 and HFF (10,000 models each) at 200-kb resolution. We used the Hi-C data available on the 4DN data portal (H1: [[https://data.4dnucleome.org/experiment-set-replicates/4DNES2M5JIGV/|4DNES2M5JIGV]], HFF: [[https://data.4dnucleome.org/experiment-set-replicates/4DNES2R6PUEK/|4DNES2R6PUEK]]). |
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| + | We then calculated the average radial positions of each 200-kb genomic region across the population (see below). The radial positions range between 0 and 1; 0 means the region is at the center of the nucleus whereas 1 means the region is at the nuclear envelope. | ||
| Average radial positions (H1): [[https://wiki.4dnucleome.org/_media/4dn:nofic_steering_committee:analysis_products:h1.avgradialpositions.txt|h1.avgradialpositions.txt]] | Average radial positions (H1): [[https://wiki.4dnucleome.org/_media/4dn:nofic_steering_committee:analysis_products:h1.avgradialpositions.txt|h1.avgradialpositions.txt]] | ||
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| ====== ====== | ====== ====== | ||
| - | ===== Loop calls ===== | ||
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| - | ===== Tad calls ===== | ||
| - | ===== Compartment calls ===== | ||
4dn/phase2/working_groups/jawg_sandbox.1590029259.txt.gz · Last modified: 2025/04/22 16:21 (external edit)