type: position_score
table:
  filename: ENCFF074WXR.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_ENCSR960JPH
  column_index: 3
  type: float
  desc: 'Histone_ChIP-seq ENCSR960JPH [biosample_summary="Homo sapiens trophoblast cell originated from H1" and target="H4K12ac"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'Histone_ChIP-seq ENCSR960JPH [biosample_summary="Homo sapiens trophoblast cell originated from H1" and target="H4K12ac"]'
  description: '**status**: released


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


    **summary**: male embryo


    **output\_type**: pseudoreplicated peaks


    **audit\_internal\_action**: Released analysis {ENCAN673LEN|/analyses/ENCAN673LEN/}
    has in progress subobject document {4adaa359-54c8-4c4c-9d6d-40b1d2666c56|/documents/4adaa359-54c8-4c4c-9d6d-40b1d2666c56/}


    **audit\_internal\_action**: Released analysis {ENCAN673LEN|/analyses/ENCAN673LEN/}
    has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/}


    **audit\_warning**: Processed alignments file {ENCFF246GMV|/files/ENCFF246GMV/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 14250423 usable fragments.
    The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H4K12ac-human and investigated as a transcription factor 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/} )


    **audit\_warning**: Processed alignments file {ENCFF829KYP|/files/ENCFF829KYP/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 15911642 usable fragments.
    The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H4K12ac-human and investigated as a transcription factor 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/} )


    **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 {ENCFF246GMV|/files/ENCFF246GMV/}
    processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF246GMV|/files/ENCFF246GMV/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.72.


    **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 {ENCFF246GMV|/files/ENCFF246GMV/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 4.15.


    **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 {ENCFF829KYP|/files/ENCFF829KYP/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library
    with NRF value of 0.79.


    **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 {ENCFF829KYP|/files/ENCFF829KYP/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.83.


    **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 {ENCFF829KYP|/files/ENCFF829KYP/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 6.55.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR960JPH
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: male embryo
    biosample_summary: Homo sapiens trophoblast cell originated from H1
    replication_type: isogenic
    biosample_ontology: /biosample-types/in_vitro_differentiated_cells_CL_0000351/
    perturbed: false
    doi: 10.17989/ENCSR960JPH
    date_created: '2015-09-16T19:17:03.987957+00:00'
    date_released: '2013-07-31'
    submitter_comment: ''
    target: H4K12ac