type: position_score
table:
  filename: ENCFF202WFY.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_ENCSR125IJY
  column_index: 3
  type: float
  desc: 'Histone_ChIP-seq ENCSR125IJY [biosample_summary="Homo sapiens SK-N-SH" and target="H3F3A"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'Histone_ChIP-seq ENCSR125IJY [biosample_summary="Homo sapiens SK-N-SH" and target="H3F3A"]'
  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 {ENCAN291VUG|/analyses/ENCAN291VUG/} has in progress\
    \ subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF754AJD|/files/ENCFF754AJD/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline has 22897336 usable fragments. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3F3A-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 alignments file {ENCFF671ZSB|/files/ENCFF671ZSB/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline has 22504933 usable fragments. The minimum\
    \ ENCODE standard for each replicate in a ChIP-seq experiment targeting H3F3A-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\\_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 {ENCFF671ZSB|/files/ENCFF671ZSB/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\
    \ PBC2 value of 9.93."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR125IJY
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens SK-N-SH
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0003072/
    perturbed: false
    doi: 10.17989/ENCSR125IJY
    date_created: '2015-05-20T20:37:38.800494+00:00'
    date_released: '2016-10-19'
    submitter_comment: ''
    target: H3F3A