type: position_score
table:
  filename: ENCFF897RQN.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_ENCSR000DQW
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000DQW [biosample_summary="Homo sapiens GM06990" and target="CTCF"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000DQW [biosample_summary="Homo sapiens GM06990" and target="CTCF"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: optimal IDR thresholded peaks\n\n**audit\\\
    _internal\\_action**: File {ENCFF897RQN|/files/ENCFF897RQN/} with status 'released'\
    \ is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'.\n\
    \n**audit\\_internal\\_action**: Archived analysis {ENCAN491WWN|/analyses/ENCAN491WWN/}\
    \ has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF545IDM|/files/ENCFF545IDM/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 7253984 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/} )\n\n**audit\\_not\\\
    _compliant**: Processed alignments file {ENCFF993RDX|/files/ENCFF993RDX/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline has 9159662 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/} )\n\n**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 {ENCFF545IDM|/files/ENCFF545IDM/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with NRF value\
    \ of 0.43.\n\n**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 {ENCFF545IDM|/files/ENCFF545IDM/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value\
    \ of 0.38.\n\n**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 {ENCFF993RDX|/files/ENCFF993RDX/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ NRF value of 0.47.\n\n**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 {ENCFF993RDX|/files/ENCFF993RDX/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value\
    \ of 0.42.\n\n**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 {ENCFF545IDM|/files/ENCFF545IDM/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC2 value of 1.41.\n\n**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 {ENCFF993RDX|/files/ENCFF993RDX/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ PBC2 value of 1.53."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000DQW
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens GM06990
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002783/
    perturbed: false
    doi: 10.17989/ENCSR000DQW
    date_created: '2014-02-12T23:06:21.292611+00:00'
    date_released: '2011-03-17'
    submitter_comment: Replicate 2,1 of this experiment was previously attributed
      to biosample ENCBS057ENC and replicate 1,1 of this experiment was previously
      attributed to biosample ENCBS057ENC but they have since been corrected to the
      current biosamples. Please note that the biosample term has remain unchanged.
    target: CTCF