type: position_score
table:
  filename: ENCFF237SGW.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_ENCSR185QFX
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR185QFX [TISSUE: Homo sapiens HEK293 genetically modified
    (insertion) using site-specific recombination targeting H. sapiens ZNF549, TARGET:
    ZNF549]'
  description: '**status**: released


    **biological\_replicates**: Rep 2, Rep 3


    **summary**: genetically modified (insertion) using site-specific recombination
    targeting H. sapiens ZNF549


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


    **audit\_internal\_action**: File {ENCFF237SGW|/files/ENCFF237SGW/} with status
    ''released'' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status
    ''archived''.


    **audit\_internal\_action**: Released analysis {ENCAN369NPT|/analyses/ENCAN369NPT/}
    has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}


    **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 {ENCFF158MHQ|/files/ENCFF158MHQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.90.


    **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 {ENCFF158MHQ|/files/ENCFF158MHQ/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 9.39.


    **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 {ENCFF364ZQY|/files/ENCFF364ZQY/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    NRF value of 0.75.


    **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 {ENCFF364ZQY|/files/ENCFF364ZQY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.75.


    **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 {ENCFF364ZQY|/files/ENCFF364ZQY/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 3.94.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR185QFX
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: genetically modified (insertion) using site-specific
      recombination targeting H. sapiens ZNF549
    biosample_summary: Homo sapiens HEK293 genetically modified (insertion) using
      site-specific recombination targeting H. sapiens ZNF549
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0001182/
    perturbed: false
    doi: 10.17989/ENCSR185QFX
    date_created: '2016-03-29T17:49:58.862183+00:00'
    date_released: '2018-07-11'
    submitter_comment: The inconsistent platform warning is due to the archived replicate
      1 fastqs being sequenced on HiSeq2000. Those files can use the pooled HiSeq2000
      controls (ENCSR598OXI) for further analysis.
    target: ZNF549