type: position_score
table:
  filename: ENCFF401ONY.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_ENCSR000DXI
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000DXI [biosample_summary="Homo sapiens bronchial epithelial cell" and target="CTCF"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000DXI [biosample_summary="Homo sapiens bronchial epithelial cell" 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\\\
    _error**: Processed alignments file {ENCFF863LNN|/files/ENCFF863LNN/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline has 4973927 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\\_internal\\\
    _action**: Archived analysis {ENCAN867UGL|/analyses/ENCAN867UGL/} has in progress\
    \ subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF902PDL|/files/ENCFF902PDL/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline has 7215863 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**: 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\
    \ {ENCFF863LNN|/files/ENCFF863LNN/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ was generated from a library with PBC1 value of 0.48.\n\n**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 {ENCFF902PDL|/files/ENCFF902PDL/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with NRF value\
    \ of 0.64.\n\n**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 {ENCFF902PDL|/files/ENCFF902PDL/} processed by ChIP-seq\
    \ ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.64.\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 {ENCFF902PDL|/files/ENCFF902PDL/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\
    \ PBC2 value of 2.77.\n\n**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 {ENCFF863LNN|/files/ENCFF863LNN/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ was generated from a library with NRF value of 0.51.\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 {ENCFF863LNN|/files/ENCFF863LNN/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\
    \ PBC2 value of 1.75."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000DXI
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens bronchial epithelial cell
    replication_type: isogenic
    biosample_ontology: /biosample-types/primary_cell_CL_0002328/
    perturbed: false
    doi: 10.17989/ENCSR000DXI
    date_created: '2013-12-19T23:39:14.744230+00:00'
    date_released: '2011-03-17'
    submitter_comment: Cross-correlation metrics are too poor to permit further analysis.
      Replicate 1,1 of this experiment was previously attributed to biosample ENCBS417ENC
      and replicate 2,1 of this experiment was previously attributed to biosample
      ENCBS417ENC but they have since been corrected to the current biosamples. Please
      note that the biosample term has remain unchanged.
    target: CTCF