type: position_score
table:
  filename: ENCFF729FSA.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_ENCSR324RCI
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR324RCI [biosample_summary="Homo sapiens liver tissue female child (4 years)" and target="FOXA1"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR324RCI [biosample_summary="Homo sapiens liver tissue female child (4 years)" and target="FOXA1"]'
  description: '**status**: released


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


    **summary**: female child (4 years)


    **output\_type**: IDR thresholded peaks


    **audit\_internal\_action**: Released analysis {ENCAN987UFD|/analyses/ENCAN987UFD/}
    has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}


    **audit\_internal\_action**: Released analysis {ENCAN987UFD|/analyses/ENCAN987UFD/}
    has in progress subobject document {6ff0d1ce-7452-471c-8557-c5ba7d72fac8|/documents/6ff0d1ce-7452-471c-8557-c5ba7d72fac8/}


    **audit\_warning**: Processed alignments file {ENCFF297KOW|/files/ENCFF297KOW/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 17968262 usable fragments.
    The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    FOXA1-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**: 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 in the range 0 - 0.5 is poor complexity, 0.5 - 0.8 is moderate
    complexity, and > 0.8 high complexity. NRF value > 0.8 is recommended, but > 0.5
    is acceptable. ENCODE processed alignments file {ENCFF297KOW|/files/ENCFF297KOW/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library
    with NRF value of 0.73.


    **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 {ENCFF297KOW|/files/ENCFF297KOW/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.73.


    **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 {ENCFF297KOW|/files/ENCFF297KOW/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 3.53.


    **audit\_warning**: Replicate concordance in ChIP-seq experiments is measured
    by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR
    thresholded peaks files {ENCFF729FSA|/files/ENCFF729FSA/} processed by ChIP-seq
    ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 1.32 and a self consistency
    ratio of 2.41. 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.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR324RCI
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: female child (4 years)
    biosample_summary: Homo sapiens liver tissue female child (4 years)
    replication_type: isogenic
    biosample_ontology: /biosample-types/tissue_UBERON_0002107/
    perturbed: false
    doi: 10.17989/ENCSR324RCI
    date_created: '2015-09-29T16:19:31.055641+00:00'
    date_released: '2016-06-30'
    submitter_comment: 'This experiment is being used in the ENCODE-DREAM Transcription
      Factor Binding Site Prediction Challenge (https://www.synapse.org/#!Synapse:syn6131484/wiki/400026).
      The files will be unavailable until after the challenge completes on 09-30-16.
      UPDATE: There will be a second round to the challenge that is expected to end
      on 01-11-2017'
    target: FOXA1