type: position_score
table:
  filename: ENCFF065PXB.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_ENCSR873EIA
  column_index: 3
  type: float
  desc: 'Histone_ChIP-seq ENCSR873EIA [biosample_summary="Homo sapiens neural cell originated from H1" and target="H3F3A"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'Histone_ChIP-seq ENCSR873EIA [biosample_summary="Homo sapiens neural cell originated from H1" and target="H3F3A"]'
  description: '**status**: released


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


    **summary**: male embryo


    **output\_type**: pseudoreplicated peaks


    **audit\_internal\_action**: Released analysis {ENCAN231CJB|/analyses/ENCAN231CJB/}
    has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/}


    **audit\_internal\_action**: Released analysis {ENCAN231CJB|/analyses/ENCAN231CJB/}
    has in progress subobject document {34741e04-2323-402a-9032-0e5b12ee9a56|/documents/34741e04-2323-402a-9032-0e5b12ee9a56/}


    **audit\_not\_compliant**: Processed alignments file {ENCFF186XXM|/files/ENCFF186XXM/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 21993631 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/})


    **audit\_not\_compliant**: Processed alignments file {ENCFF073IRJ|/files/ENCFF073IRJ/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 16119334 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/})


    **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 {ENCFF186XXM|/files/ENCFF186XXM/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library
    with NRF value of 0.49.


    **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 {ENCFF186XXM|/files/ENCFF186XXM/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.46.


    **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 {ENCFF186XXM|/files/ENCFF186XXM/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 1.75.


    **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 {ENCFF073IRJ|/files/ENCFF073IRJ/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library
    with NRF value of 0.75.


    **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 {ENCFF073IRJ|/files/ENCFF073IRJ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.73.


    **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 {ENCFF073IRJ|/files/ENCFF073IRJ/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 3.55.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR873EIA
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: male embryo
    biosample_summary: Homo sapiens neural cell originated from H1
    replication_type: isogenic
    biosample_ontology: /biosample-types/in_vitro_differentiated_cells_CL_0002319/
    perturbed: false
    doi: 10.17989/ENCSR873EIA
    date_created: '2014-12-05T21:17:17.609771+00:00'
    date_released: '2016-10-25'
    submitter_comment: As of June 22, 2017, control ENCSR308JFE requires new bams.
      New files will be processed for its downstream experiments.
    target: H3F3A