type: position_score
table:
  filename: ENCFF731UCU.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_ENCSR967HXD
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR967HXD [TISSUE: Homo sapiens H9 stably expressing HES5,
    TARGET: H3K4me1]'
  description: '**status**: released


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


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


    **output\_type**: pseudoreplicated peaks


    **audit\_internal\_action**: Released analysis {ENCAN240BQK|/analyses/ENCAN240BQK/}
    has in progress subobject document {cf44fa62-50ae-4eb1-aeb9-6403fd645dee|/documents/cf44fa62-50ae-4eb1-aeb9-6403fd645dee/}


    **audit\_internal\_action**: Released analysis {ENCAN240BQK|/analyses/ENCAN240BQK/}
    has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/}


    **audit\_not\_compliant**: Processed alignments file {ENCFF695XNX|/files/ENCFF695XNX/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 34215070 usable fragments.
    The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H3K4me1-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**: Processed alignments file {ENCFF418IUS|/files/ENCFF418IUS/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 35789340 usable fragments.
    The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H3K4me1-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**: 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 {ENCFF695XNX|/files/ENCFF695XNX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.88.


    **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 {ENCFF695XNX|/files/ENCFF695XNX/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 7.98.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR967HXD
    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/ENCSR967HXD
    date_created: '2015-10-02T22:24:12.436798+00:00'
    date_released: '2016-05-20'
    submitter_comment: ''
    target: H3K4me1