type: position_score
table:
  filename: ENCFF861NDU.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: TF_ChIP-seq_ENCSR000DND
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000DND [biosample_summary="Homo sapiens pancreas tissue male adult (54 years) and male adult (60 years)" and target="CTCF"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000DND [biosample_summary="Homo sapiens pancreas tissue male adult (54 years) and male adult (60 years)" and target="CTCF"]'
  description: '**status**: released


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


    **summary**: male adult (54 years) male adult (60 years)


    **output\_type**: optimal IDR thresholded peaks


    **audit\_internal\_action**: File {ENCFF861NDU|/files/ENCFF861NDU/} with status
    ''released'' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status
    ''archived''.


    **audit\_internal\_action**: Archived analysis {ENCAN153QZB|/analyses/ENCAN153QZB/}
    has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}


    **audit\_error**: Processed alignments file {ENCFF018QYS|/files/ENCFF018QYS/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 3796817 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    CTCF-human and investigated as a transcription factor is 10 million usable fragments.
    The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE
    ChIP-seq data standards|/data-standards/chip-seq/} )


    **audit\_error**: Processed alignments file {ENCFF753GJH|/files/ENCFF753GJH/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 3806459 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    CTCF-human and investigated as a transcription factor is 10 million usable fragments.
    The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE
    ChIP-seq data standards|/data-standards/chip-seq/} )


    **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 > 0.8 is acceptable. ENCODE processed alignments
    file {ENCFF018QYS|/files/ENCFF018QYS/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.87.


    **audit\_warning**: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio
    of the number of genomic locations where exactly one read maps uniquely (M1) to
    the number of genomic locations where two reads map uniquely (M2). A PBC2 value
    in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3
    - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended,
    but > 3 is acceptable. ENCODE processed alignments file {ENCFF018QYS|/files/ENCFF018QYS/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 7.84.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000DND
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: male adult (54 years) male adult (60 years)
    biosample_summary: Homo sapiens pancreas tissue male adult (54 years) and male
      adult (60 years)
    replication_type: anisogenic
    biosample_ontology: /biosample-types/tissue_UBERON_0001264/
    perturbed: false
    doi: 10.17989/ENCSR000DND
    date_created: '2013-09-13T16:53:24.172874-08:00'
    date_released: '2012-08-27'
    submitter_comment: ''
    target: CTCF
