type: position_score
table:
  filename: ENCFF868BIT.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_ENCSR000DJW
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000DJW [biosample_summary="Homo sapiens K562 stably expressing NR4A1" and target="NR4A1"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000DJW [biosample_summary="Homo sapiens K562 stably expressing NR4A1" and target="NR4A1"]'
  description: '**status**: released


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


    **summary**: stably expressing NR4A1


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


    **audit\_internal\_action**: File {ENCFF868BIT|/files/ENCFF868BIT/} with status
    ''released'' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status
    ''archived''.


    **audit\_internal\_action**: Archived analysis {ENCAN516CZC|/analyses/ENCAN516CZC/}
    has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}


    **audit\_not\_compliant**: Replicate concordance in ChIP-seq experiments is measured
    by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR
    thresholded peaks files {ENCFF468APC|/files/ENCFF468APC/}, {ENCFF171BKD|/files/ENCFF171BKD/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 14.48 and
    a self consistency ratio of 2.82. According to ENCODE standards, having both rescue
    ratio and self consistency ratio values < 2 is recommended, but having only one
    of the ratio values < 2 is acceptable.


    **audit\_not\_compliant**: Replicate concordance in ChIP-seq experiments is measured
    by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR
    thresholded peaks files {ENCFF002VSM|/files/ENCFF002VSM/}, {ENCFF868BIT|/files/ENCFF868BIT/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 14.48 and
    a self consistency ratio of 2.82. According to ENCODE standards, having both rescue
    ratio and self consistency ratio values < 2 is recommended, but having only one
    of the ratio values < 2 is acceptable.


    **audit\_warning**: Processed alignments file {ENCFF602UAC|/files/ENCFF602UAC/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 19266769 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    NR4A1-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**: Processed alignments file {ENCFF650RFL|/files/ENCFF650RFL/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 15853862 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    NR4A1-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/} )'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000DJW
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: stably expressing NR4A1
    biosample_summary: Homo sapiens K562 stably expressing NR4A1
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002067/
    perturbed: false
    doi: 10.17989/ENCSR000DJW
    date_created: '2014-02-12T23:27:58.527633+00:00'
    date_released: '2011-06-03'
    submitter_comment: ''
    target: NR4A1
