type: position_score
table:
  filename: ENCFF431GJK.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_ENCSR178DEG
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR178DEG [biosample_summary="Homo sapiens K562 stably expressing NR2C1" and target="NR2C1"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR178DEG [biosample_summary="Homo sapiens K562 stably expressing NR2C1" and target="NR2C1"]'
  description: '**status**: released


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


    **summary**: stably expressing C-terminal eGFP-tagged NR2C1


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


    **audit\_internal\_action**: Archived analysis {ENCAN914XJJ|/analyses/ENCAN914XJJ/}
    has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}


    **audit\_internal\_action**: File {ENCFF431GJK|/files/ENCFF431GJK/} with status
    ''released'' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status
    ''archived''.


    **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 {ENCFF285CII|/files/ENCFF285CII/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.83.


    **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 {ENCFF285CII|/files/ENCFF285CII/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 5.72.


    **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 {ENCFF096KBP|/files/ENCFF096KBP/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.84.


    **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 {ENCFF096KBP|/files/ENCFF096KBP/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 6.27.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR178DEG
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: stably expressing C-terminal eGFP-tagged NR2C1
    biosample_summary: Homo sapiens K562 stably expressing NR2C1
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002067/
    perturbed: false
    doi: 10.17989/ENCSR178DEG
    date_created: '2015-10-31T21:07:32.483071+00:00'
    date_released: '2017-01-31'
    submitter_comment: Please note that the 'mixed platform' warning comes from the
      archived fastqs that were sequenced on the HiSeq2000 platform that if used,
      should be paired with the matching HiSeq2000 control ENCSR805ITZ. The pipeline
      was run on the fastqs and controls sequenced on the HiSeq4000 platform for consistency.
    target: NR2C1
