type: position_score
table:
  filename: ENCFF925HDQ.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_ENCSR870IUC
  column_index: 3
  type: float
  desc: 'Histone_ChIP-seq ENCSR870IUC [biosample_summary="Homo sapiens H9 stably expressing HES5" and target="H3K36me3"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'Histone_ChIP-seq ENCSR870IUC [biosample_summary="Homo sapiens H9 stably expressing HES5" and target="H3K36me3"]'
  description: '**status**: released


    **biological\_replicates**: Rep 1, Rep 2


    **summary**: stably expressing C-terminal eGFP-tagged HES5


    **output\_type**: replicated peaks


    **audit\_internal\_action**: Archived analysis {ENCAN864FCP|/analyses/ENCAN864FCP/}
    has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/}


    **audit\_not\_compliant**: Processed alignments file {ENCFF990UKW|/files/ENCFF990UKW/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 29557144 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H3K36me3-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/})


    **audit\_not\_compliant**: Processed alignments file {ENCFF364UEA|/files/ENCFF364UEA/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 9625420 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H3K36me3-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/})


    **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 {ENCFF364UEA|/files/ENCFF364UEA/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    NRF value of 0.61.


    **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 {ENCFF364UEA|/files/ENCFF364UEA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.58.


    **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 {ENCFF364UEA|/files/ENCFF364UEA/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 2.23.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR870IUC
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: stably expressing C-terminal eGFP-tagged HES5
    biosample_summary: Homo sapiens H9 stably expressing HES5
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0003045/
    perturbed: false
    doi: 10.17989/ENCSR870IUC
    date_created: '2015-10-02T22:24:47.623006+00:00'
    date_released: '2016-05-20'
    submitter_comment: ''
    target: H3K36me3