type: position_score
table:
  filename: ENCFF434OEY.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_ENCSR000AUZ
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000AUZ [biosample_summary="Homo sapiens B cell female adult (27 years)" and target="EZH2"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000AUZ [biosample_summary="Homo sapiens B cell female adult (27 years)" and target="EZH2"]'
  description: '**status**: released


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


    **summary**: female adult (27 years)


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


    **audit\_error**: Processed alignments file {ENCFF563GAI|/files/ENCFF563GAI/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 4688845 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    EZH2-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\_internal\_action**: Archived analysis {ENCAN474ANX|/analyses/ENCAN474ANX/}
    has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}


    **audit\_internal\_action**: File {ENCFF434OEY|/files/ENCFF434OEY/} with status
    ''released'' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status
    ''archived''.


    **audit\_not\_compliant**: 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 {ENCFF563GAI|/files/ENCFF563GAI/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    NRF value of 0.27.


    **audit\_not\_compliant**: 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 {ENCFF563GAI|/files/ENCFF563GAI/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.30.


    **audit\_warning**: Processed alignments file {ENCFF301OCC|/files/ENCFF301OCC/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 17009288 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    EZH2-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**: 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 {ENCFF563GAI|/files/ENCFF563GAI/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 1.83.


    **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 {ENCFF301OCC|/files/ENCFF301OCC/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    NRF value of 0.69.


    **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 {ENCFF301OCC|/files/ENCFF301OCC/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.68.


    **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 {ENCFF301OCC|/files/ENCFF301OCC/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 3.08.


    **audit\_warning**: Replicate concordance in ChIP-seq experiments is measured
    by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR
    thresholded peaks files {ENCFF741FOY|/files/ENCFF741FOY/}, {ENCFF434OEY|/files/ENCFF434OEY/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.92 and
    a self consistency ratio of 12.09. 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**: Replicate concordance in ChIP-seq experiments is measured
    by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR
    thresholded peaks files {ENCFF463JXZ|/files/ENCFF463JXZ/}, {ENCFF161HRO|/files/ENCFF161HRO/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.92 and
    a self consistency ratio of 12.09. 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: ENCSR000AUZ
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: female adult (27 years)
    biosample_summary: Homo sapiens B cell female adult (27 years)
    replication_type: isogenic
    biosample_ontology: /biosample-types/primary_cell_CL_0000236/
    perturbed: false
    doi: 10.17989/ENCSR000AUZ
    date_created: '2013-11-07T22:16:05.858177+00:00'
    date_released: '2012-08-06'
    submitter_comment: ''
    target: EZH2
