type: position_score
table:
  filename: ENCFF498EED.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_ENCSR000DMC
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR000DMC [TISSUE: Homo sapiens kidney tissue male adult (22
    years) and male adult (27 years) and male adult (35 years), TARGET: CTCF]'
  description: '**status**: released


    **biological\_replicates**: Rep 1, Rep 2, Rep 3


    **summary**: male adult (27 years) male adult (22 years) male adult (35 years)


    **output\_type**: IDR thresholded peaks


    **audit\_error**: Processed alignments file {ENCFF402MXP|/files/ENCFF402MXP/}
    processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 2815191 usable fragments.
    The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    CTCF-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**: Released analysis {ENCAN790ONI|/analyses/ENCAN790ONI/}
    has in progress subobject document {b8b9cf14-23a2-4c0d-8304-8b0c7b31c20b|/documents/b8b9cf14-23a2-4c0d-8304-8b0c7b31c20b/}


    **audit\_internal\_action**: Released analysis {ENCAN790ONI|/analyses/ENCAN790ONI/}
    has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}


    **audit\_not\_compliant**: Processed alignments file {ENCFF110ZAA|/files/ENCFF110ZAA/}
    processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 5229631 usable fragments.
    The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    CTCF-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\_not\_compliant**: Processed alignments file {ENCFF129BYY|/files/ENCFF129BYY/}
    processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 5176864 usable fragments.
    The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    CTCF-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**: 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 {ENCFF110ZAA|/files/ENCFF110ZAA/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.87.


    **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 {ENCFF110ZAA|/files/ENCFF110ZAA/}
    processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 7.56.


    **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 {ENCFF402MXP|/files/ENCFF402MXP/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.89.


    **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 {ENCFF402MXP|/files/ENCFF402MXP/}
    processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 9.37.


    **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 {ENCFF129BYY|/files/ENCFF129BYY/}
    processed by ChIP-seq ENCODE4 v1.5.1 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 {ENCFF129BYY|/files/ENCFF129BYY/} processed by ChIP-seq ENCODE4 v1.5.1 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 {ENCFF129BYY|/files/ENCFF129BYY/}
    processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 4.15.


    **audit\_warning**: Replicate concordance in ChIP-seq experiments is measured
    by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR
    thresholded peaks files {ENCFF498EED|/files/ENCFF498EED/} processed by ChIP-seq
    ENCODE4 v1.5.1 GRCh38 pipeline have a rescue ratio of 1.31 and a self consistency
    ratio of 7.29. 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 {ENCFF335EKK|/files/ENCFF335EKK/} processed by ChIP-seq
    ENCODE4 v1.5.1 GRCh38 pipeline have a rescue ratio of 1.31 and a self consistency
    ratio of 7.29. 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: ENCSR000DMC
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: male adult (27 years) male adult (35 years) male adult
      (22 years)
    biosample_summary: Homo sapiens kidney tissue male adult (22 years) and male adult
      (27 years) and male adult (35 years)
    replication_type: anisogenic
    biosample_ontology: /biosample-types/tissue_UBERON_0002113/
    perturbed: false
    doi: 10.17989/ENCSR000DMC
    date_created: '2013-09-13T16:53:23.770566-08:00'
    date_released: '2012-08-27'
    submitter_comment: ''
    target: CTCF
