type: position_score
table:
  filename: ENCFF055NNT.tabix.bed.gz
  header_mode: none
  zero_based: true
  format: tabix
  chrom:
    column_index: 0
  pos_begin:
    column_index: 1
  pos_end:
    column_index: 2
scores:
- id: ATAC-seq_ENCSR859USB
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR859USB [TISSUE: Homo sapiens K562]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: replicated peaks\n\n**audit\\_error**: Alignment\
    \ file {ENCFF557RSA|/files/ENCFF557RSA/} processed by ATAC-seq ENCODE4 v2.1.1\
    \ GRCh38 pipeline has 8585759 usable fragments. According to ENCODE4 standards,\
    \ ATAC-seq assays processed by the uniform processing pipeline should have > 25\
    \ million usable fragments. 20-25 million is acceptable and < 15 million is not\
    \ compliant.\n\n**audit\\_internal\\_action**: Released analysis {ENCAN615CMZ|/analyses/ENCAN615CMZ/}\
    \ has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}\n\
    \n**audit\\_not\\_compliant**: Alignment file {ENCFF852RRY|/files/ENCFF852RRY/}\
    \ processed by ATAC-seq ENCODE4 v2.1.1 GRCh38 pipeline has 15065125 usable fragments.\
    \ According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing\
    \ pipeline should have > 25 million usable fragments. 20-25 million is acceptable\
    \ and < 15 million is not compliant.\n\n**audit\\_warning**: According to ENCODE4\
    \ standards, ATAC-seq assays processed by the uniform processing pipeline should\
    \ have either >150k reproducible peaks in an overlap peaks file, or >70k in an\
    \ IDR thresholded peaks file. 100-150k or 50-70k peaks respectively is acceptable,\
    \ and <100k or <50k respectively is not compliant. File(s) {ENCFF055NNT|/files/ENCFF055NNT/}\
    \ (overlap peaks) and {ENCFF926KTI|/files/ENCFF926KTI/} (IDR thresholded peaks)\
    \ processed by ATAC-seq ENCODE4 v2.1.1 GRCh38 pipeline have 99862 and 55575 peaks."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR859USB
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens K562
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002067/
    perturbed: false
    doi: 10.17989/ENCSR859USB
    date_created: '2021-03-15T22:05:23.257090+00:00'
    date_released: '2022-04-26'
    submitter_comment: ''