type: position_score
table:
  filename: ENCFF034USW.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_ENCSR000DUO
  column_index: 3
  type: float
  desc: 'Histone_ChIP-seq ENCSR000DUO [biosample_summary="Homo sapiens HL-60" and target="H3K4me3"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'Histone_ChIP-seq ENCSR000DUO [biosample_summary="Homo sapiens HL-60" and target="H3K4me3"]'
  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 {ENCAN506YWM|/analyses/ENCAN506YWM/} has in progress\
    \ subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF693QTE|/files/ENCFF693QTE/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 7623406 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3K4me3-human and investigated as a narrow histone mark 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 {ENCFF355WJQ|/files/ENCFF355WJQ/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 9161715 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3K4me3-human and investigated as a narrow histone mark 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\
    \ {ENCFF693QTE|/files/ENCFF693QTE/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ was generated from a library with PBC1 value of 0.85.\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 {ENCFF693QTE|/files/ENCFF693QTE/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ PBC2 value of 6.95.\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 {ENCFF355WJQ|/files/ENCFF355WJQ/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value\
    \ of 0.86.\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 {ENCFF355WJQ|/files/ENCFF355WJQ/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC2 value of 7.20."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000DUO
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens HL-60
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002793/
    perturbed: false
    doi: 10.17989/ENCSR000DUO
    date_created: '2014-02-12T23:17:21.304163+00:00'
    date_released: '2011-02-11'
    submitter_comment: Replicate 1,1 of this experiment was previously attributed
      to biosample ENCBS069ENC and replicate 2,1 of this experiment was previously
      attributed to biosample ENCBS069ENC but they have since been corrected to the
      current biosamples. Please note that the biosample term has remain unchanged.
    target: H3K4me3