| source_audit: data/external/k562_molecular_sources_audit.yaml |
| target_assembly: hg19 |
| candidate_contact_sources: 2 |
| candidate_contact_matrices: 1 |
| ready_contact_matrices: 0 |
| plan_records: |
| - family: reference_hic |
| accession: ENCFF621AIY |
| assembly: GRCh38 |
| file_format: hic |
| output_type: mapping quality thresholded contact matrix |
| status: released |
| file_size: 33783625697 |
| md5sum: 71e5dc072beddbdcda11c9016696e142 |
| download_url: https://www.encodeproject.org/files/ENCFF621AIY/@@download/ENCFF621AIY.hic |
| s3_uri: s3://encode-public/2022/05/15/0571c671-3645-4f92-beae-51dfd3f42c36/ENCFF621AIY.hic |
| local_path: data/raw/k562_molecular/reference_hic/ENCFF621AIY.hic |
| local_exists: false |
| action: requires_assembly_strategy_before_use |
| - family: reference_hic |
| accession: ENCFF134PUN |
| assembly: GRCh38 |
| file_format: bed |
| output_type: contact domains |
| status: archived |
| file_size: 58070147883 |
| md5sum: cd12d922bb71692d98f924c04e72d038 |
| download_url: https://www.encodeproject.org/files/ENCFF134PUN/@@download/ENCFF134PUN.bed.gz |
| s3_uri: s3://encode-public/2023/04/12/9c79af08-d830-4e4d-ae35-bae09c98b328/ENCFF134PUN.bed.gz |
| local_path: data/raw/k562_molecular/reference_hic/ENCFF134PUN.bed.gz |
| local_exists: false |
| action: not_a_contact_matrix |
| recommended_next_action: 'No assembly-matched local contact matrix is ready. Current |
| ENCODE K562 .hic candidate is GRCh38 while the Gasperini benchmark is treated as |
| hg19. Choose one controlled path: create a GRCh38/liftOver candidate table with |
| QC, or use an hg19-compatible contact source. Then dump sparse pixels and run scripts/build_k562_contact_features.py.' |
| example_sparse_build_command: PYTHONPATH=src .venv/bin/python scripts/build_k562_contact_features.py |
| --contacts data/interim/k562_contacts/k562_10kb_pixels.tsv.gz --contact-assembly |
| hg19 --resolution-bp 10000 |
|
|
