type: position_score
table:
  filename: ENCFF089MEL.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_ENCSR331JFZ
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR331JFZ [TISSUE: Homo sapiens HG03575]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1\n\n**summary**:\
    \ \n\n**output\\_type**: pseudoreplicated peaks\n\n**audit\\_error**: Alignment\
    \ file {ENCFF632MBC|/files/ENCFF632MBC/} processed by ATAC-seq ENCODE4 v1.9.1\
    \ GRCh38 pipeline has 12592755 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 {ENCAN086FNR|/analyses/ENCAN086FNR/}\
    \ has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}\n\
    \n**audit\\_not\\_compliant**: According to ENCODE4 standards, overlap peaks files\
    \ in ATAC-seq assays processed by the uniform processing pipeline should have\
    \ FRiP (fraction of reads in called peak regions) scores > 0.3. FRiP scores 0.2-0.3\
    \ are acceptable, and < 0.2 are not compliant. {ENCFF089MEL|/files/ENCFF089MEL/}\
    \ processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline  has a FRiP score of 0.19.\n\
    \n**audit\\_not\\_compliant**: 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) {ENCFF089MEL|/files/ENCFF089MEL/} (overlap peaks) and\
    \ {ENCFF027KMZ|/files/ENCFF027KMZ/} (IDR thresholded peaks) processed by ATAC-seq\
    \ ENCODE4 v1.9.1 GRCh38 pipeline have 98877 and 38973 peaks."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR331JFZ
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens HG03575
    replication_type: unreplicated
    biosample_ontology: /biosample-types/cell_line_EFO_0010890/
    perturbed: false
    doi: 10.17989/ENCSR331JFZ
    date_created: '2020-11-24T22:02:43.513868+00:00'
    date_released: '2021-02-11'
    submitter_comment: ''
