type: position_score
table:
  filename: ENCFF609DIL.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_ENCSR958ZMM
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR958ZMM [TISSUE: Homo sapiens neural cell originated from
    H1, TARGET: H4K20me1]'
  description: '**status**: released


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


    **summary**: male embryo


    **output\_type**: pseudoreplicated peaks


    **audit\_internal\_action**: Released analysis {ENCAN984HRJ|/analyses/ENCAN984HRJ/}
    has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/}


    **audit\_internal\_action**: Released analysis {ENCAN984HRJ|/analyses/ENCAN984HRJ/}
    has in progress subobject document {ce9320b4-7c32-4e7f-bcd4-a8b9c81dba92|/documents/ce9320b4-7c32-4e7f-bcd4-a8b9c81dba92/}


    **audit\_not\_compliant**: Processed alignments file {ENCFF136JPJ|/files/ENCFF136JPJ/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 31222385 usable fragments.
    The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H4K20me1-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 {ENCFF682KHR|/files/ENCFF682KHR/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 23013539 usable fragments.
    The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H4K20me1-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 {ENCFF682KHR|/files/ENCFF682KHR/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.85.


    **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 {ENCFF682KHR|/files/ENCFF682KHR/}
    processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 6.67.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR958ZMM
    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/ENCSR958ZMM
    date_created: '2014-10-24T16:17:21.510735+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: H4K20me1
