File size: 1,840 Bytes
4504783 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | 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
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