type: position_score
table:
  filename: ENCFF314ZAL.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_ENCSR000DTW
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR000DTW [TISSUE: Homo sapiens HEK293, 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 {ENCFF018VMV|/files/ENCFF018VMV/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline has 4808648 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 {ENCAN114IXY|/analyses/ENCAN114IXY/} has in progress\
    \ subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_internal\\_action**: File {ENCFF314ZAL|/files/ENCFF314ZAL/} with status\
    \ 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status\
    \ 'archived'.\n\n**audit\\_warning**: Processed alignments file {ENCFF594YMC|/files/ENCFF594YMC/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 10402269 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\\_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\
    \ {ENCFF018VMV|/files/ENCFF018VMV/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ was generated from a library with PBC1 value of 0.90.\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 {ENCFF018VMV|/files/ENCFF018VMV/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ PBC2 value of 9.81.\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 {ENCFF594YMC|/files/ENCFF594YMC/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with NRF value of 0.78.\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\
    \ {ENCFF594YMC|/files/ENCFF594YMC/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ was generated from a library with PBC1 value of 0.82.\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 {ENCFF594YMC|/files/ENCFF594YMC/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ PBC2 value of 6.61.\n\n**audit\\_warning**: Replicate concordance in ChIP-seq\
    \ experiments is measured by calculating IDR values (Irreproducible Discovery\
    \ Rate). ENCODE processed IDR thresholded peaks files {ENCFF033KSK|/files/ENCFF033KSK/},\
    \ {ENCFF530VSC|/files/ENCFF530VSC/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ have a rescue ratio of 1.19 and a self consistency ratio of 2.01. 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.\n\
    \n**audit\\_warning**: Replicate concordance in ChIP-seq experiments is measured\
    \ by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed\
    \ IDR thresholded peaks files {ENCFF314ZAL|/files/ENCFF314ZAL/}, {ENCFF008LSM|/files/ENCFF008LSM/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.19 and\
    \ a self consistency ratio of 2.01. 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: ENCSR000DTW
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens HEK293
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0001182/
    perturbed: false
    doi: 10.17989/ENCSR000DTW
    date_created: '2014-02-12T23:22:23.775092+00:00'
    date_released: '2011-03-17'
    submitter_comment: Replicate 1,1 of this experiment was previously attributed
      to biosample ENCBS393ENC but it has since been corrected to the current biosample.
      Please note that the biosample term has remain unchanged.
    target: CTCF