type: position_score
table:
  filename: ENCFF259KAD.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_ENCSR634OAQ
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR634OAQ [biosample_summary="Homo sapiens NCI-H929" and target="CTCF"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR634OAQ [biosample_summary="Homo sapiens NCI-H929" 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**: Archived analysis {ENCAN270FJU|/analyses/ENCAN270FJU/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_internal\\_action**: File {ENCFF259KAD|/files/ENCFF259KAD/} with status\
    \ 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status\
    \ 'archived'.\n\n**audit\\_not\\_compliant**: Processed alignments file {ENCFF053VXH|/files/ENCFF053VXH/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 8306834 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 {ENCFF053VXH|/files/ENCFF053VXH/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ NRF value of 0.39.\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 {ENCFF053VXH|/files/ENCFF053VXH/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value\
    \ of 0.40.\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 {ENCFF803MUP|/files/ENCFF803MUP/} processed by ChIP-seq\
    \ ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.87.\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 {ENCFF803MUP|/files/ENCFF803MUP/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ PBC2 value of 7.63.\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 {ENCFF053VXH|/files/ENCFF053VXH/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC2 value of 1.78."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR634OAQ
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens NCI-H929
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0001221/
    perturbed: false
    doi: 10.17989/ENCSR634OAQ
    date_created: '2015-05-19T17:02:56.904313+00:00'
    date_released: '2017-11-29'
    submitter_comment: One of the replicates was much higher quality than the other.
    target: CTCF