type: position_score
table:
  filename: ENCFF407NOE.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: Histone_ChIP-seq_ENCSR523BMU
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR523BMU [TISSUE: Homo sapiens CD4-positive, CD25-positive,
    alpha-beta regulatory T cell, TARGET: H3K4me1]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: replicated peaks\n\n**audit\\_internal\\\
    _action**: Archived analysis {ENCAN899NQX|/analyses/ENCAN899NQX/} has in progress\
    \ subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF671UFH|/files/ENCFF671UFH/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline has 8441657 usable fragments. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3K4me1-human and investigated as a broad histone mark is 20 million usable\
    \ fragments. The recommended value is > 45 million, but > 35 million is acceptable.\
    \ (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/})\n\n**audit\\\
    _not\\_compliant**: Processed redacted alignments file {ENCFF582DXU|/files/ENCFF582DXU/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline has 7017919 usable fragments. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3K4me1-human and investigated as a broad histone mark is 20 million usable\
    \ fragments. The recommended value is > 45 million, but > 35 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 {ENCFF671UFH|/files/ENCFF671UFH/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ was generated from a library with PBC1 value of 0.46.\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 redacted alignments file {ENCFF582DXU|/files/ENCFF582DXU/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\
    \ NRF value of 0.31.\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 redacted alignments file {ENCFF582DXU|/files/ENCFF582DXU/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\
    \ PBC1 value of 0.33.\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 {ENCFF671UFH|/files/ENCFF671UFH/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ was generated from a library with NRF value of 0.50.\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 {ENCFF671UFH|/files/ENCFF671UFH/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\
    \ PBC2 value of 1.70.\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 redacted\
    \ alignments file {ENCFF582DXU|/files/ENCFF582DXU/} processed by ChIP-seq ENCODE3\
    \ hg19 pipeline was generated from a library with PBC2 value of 1.83."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR523BMU
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens CD4-positive, CD25-positive, alpha-beta regulatory
      T cell
    replication_type: anisogenic
    biosample_ontology: /biosample-types/primary_cell_CL_0000792/
    perturbed: false
    doi: 10.17989/ENCSR523BMU
    date_created: '2015-09-15T19:48:48.720133+00:00'
    date_released: '2013-07-31'
    submitter_comment: The raw data from at least one replicate is not available to
      the ENCODE consortium. As of January 22, 2018, this experiment has been re-released
      as a replicated experiment.
    target: H3K4me1