type: position_score
table:
  filename: ENCFF858SAF.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: TF_ChIP-seq_ENCSR123GPC
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR123GPC [TISSUE: Homo sapiens HepG2 genetically modified
    (insertion) using CRISPR targeting H. sapiens THAP9, TARGET: THAP9]'
  description: '**status**: released


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


    **summary**: genetically modified (insertion) using CRISPR targeting H. sapiens
    THAP9


    **output\_type**: IDR thresholded peaks


    **audit\_internal\_action**: Released file {ENCFF858SAF|/files/ENCFF858SAF/} has
    deleted subobject file {ENCFF586OVX|/files/ENCFF586OVX/}


    **audit\_internal\_action**: Released analysis {ENCAN398OYO|/analyses/ENCAN398OYO/}
    has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}


    **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 {ENCFF858PRY|/files/ENCFF858PRY/} processed by ChIP-seq ENCODE4 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.84.


    **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 {ENCFF858PRY|/files/ENCFF858PRY/}
    processed by ChIP-seq ENCODE4 GRCh38 pipeline was generated from a library with
    PBC2 value of 6.19.


    **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 {ENCFF514XNY|/files/ENCFF514XNY/} processed by ChIP-seq ENCODE4 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.89.


    **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 {ENCFF514XNY|/files/ENCFF514XNY/}
    processed by ChIP-seq ENCODE4 GRCh38 pipeline was generated from a library with
    PBC2 value of 9.03.


    **audit\_warning**: Replicate concordance in ChIP-seq experiments is measured
    by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR
    thresholded peaks files {ENCFF858SAF|/files/ENCFF858SAF/} processed by ChIP-seq
    ENCODE4 GRCh38 pipeline have a rescue ratio of 1.39 and a self consistency ratio
    of 4.68. According to ENCODE standards, having both rescue ratio and self consistency
    ratio values < 2 is recommended, but having only one of the ratio values < 2 is
    acceptable.


    **audit\_warning**: Replicate concordance in ChIP-seq experiments is measured
    by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR
    thresholded peaks files {ENCFF687WSR|/files/ENCFF687WSR/} processed by ChIP-seq
    ENCODE4 GRCh38 pipeline have a rescue ratio of 1.39 and a self consistency ratio
    of 4.68. According to ENCODE standards, having both rescue ratio and self consistency
    ratio values < 2 is recommended, but having only one of the ratio values < 2 is
    acceptable.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR123GPC
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: genetically modified (insertion) using CRISPR targeting
      H. sapiens THAP9
    biosample_summary: Homo sapiens HepG2 genetically modified (insertion) using CRISPR
      targeting H. sapiens THAP9
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0001187/
    perturbed: false
    doi: 10.17989/ENCSR123GPC
    date_created: '2019-07-08T15:29:50.983882+00:00'
    date_released: '2020-08-21'
    submitter_comment: ''
    target: THAP9