type: position_score
table:
  filename: ENCFF105ZAX.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_ENCSR032MEH
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR032MEH [TISSUE: Homo sapiens T-cell male adult (43 years)]'
  description: '**status**: released


    **biological\_replicates**: Rep 1, Rep 2


    **summary**: male adult (43 years)


    **output\_type**: pseudoreplicated peaks


    **audit\_internal\_action**: Released analysis {ENCAN854QMS|/analyses/ENCAN854QMS/}
    has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}


    **audit\_not\_compliant**: Transcription Start Site (TSS) enrichment values for
    alignments to the human genome GRCh38 are concerning when < 5, acceptable between
    5 and 7, and ideal when > 7. ENCODE processed file {ENCFF400ZNW|/files/ENCFF400ZNW/}
    processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has a TSS enrichment value
    of 1.9192740289086339.


    **audit\_not\_compliant**: Transcription Start Site (TSS) enrichment values for
    alignments to the human genome GRCh38 are concerning when < 5, acceptable between
    5 and 7, and ideal when > 7. ENCODE processed file {ENCFF410WTM|/files/ENCFF410WTM/}
    processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has a TSS enrichment value
    of 2.010155365758926.


    **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. {ENCFF105ZAX|/files/ENCFF105ZAX/} processed
    by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline  has a FRiP score of 0.05.


    **audit\_warning**: NRF (Non Redundant Fraction) is equal to the result of the
    division of the number of reads after duplicates removal by the total number of
    reads. An NRF value < 0.7 is poor complexity, between 0.7 and 0.9 is moderate
    complexity, and >= 0.9 high complexity. NRF value > 0.9 is recommended, but >
    0.7 is acceptable. ENCODE processed file {ENCFF410WTM|/files/ENCFF410WTM/} processed
    by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with
    NRF value of 0.794959.


    **audit\_warning**: PBC1 (PCR Bottlenecking Coefficient 1, M1/M\_distinct) is
    the ratio of the number of genomic locations where  exactly one read maps uniquely
    (M1) to the number of genomic locations where some reads map (M\_distinct). A
    PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate
    bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking.
    PBC1 value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file
    {ENCFF410WTM|/files/ENCFF410WTM/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38
    pipeline was generated from a library with a PBC1 value of 0.79.


    **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) {ENCFF105ZAX|/files/ENCFF105ZAX/} (overlap peaks) and {ENCFF206PEF|/files/ENCFF206PEF/}
    (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline
    have 105476 and 1703 peaks.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR032MEH
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: male adult (43 years)
    biosample_summary: Homo sapiens T-cell male adult (43 years)
    replication_type: isogenic
    biosample_ontology: /biosample-types/primary_cell_CL_0000084/
    perturbed: false
    doi: 10.17989/ENCSR032MEH
    date_created: '2021-07-14T17:33:28.171774+00:00'
    date_released: '2022-06-08'
    submitter_comment: This dataset has been released as part of a larger biosample
      and assay collection, despite noncompliance with ENCODE quality standards, due
      to lack of sample material to reattempt the assay.
