type: position_score
table:
  filename: ENCFF404EVY.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_ENCSR497VFH
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR497VFH [biosample_summary="Homo sapiens K562" and target="ZNF639"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR497VFH [biosample_summary="Homo sapiens K562" and target="ZNF639"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: optimal IDR thresholded peaks\n\n**audit\\\
    _internal\\_action**: File {ENCFF404EVY|/files/ENCFF404EVY/} with status 'released'\
    \ is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'.\n\
    \n**audit\\_internal\\_action**: Archived analysis {ENCAN590XYM|/analyses/ENCAN590XYM/}\
    \ has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_warning**: Processed alignments file {ENCFF411KAB|/files/ENCFF411KAB/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 19273399 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ ZNF639-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/} )\n\n**audit\\\
    _warning**: Replicate concordance in ChIP-seq experiments is measured by calculating\
    \ IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded\
    \ peaks files {ENCFF947YGS|/files/ENCFF947YGS/}, {ENCFF404EVY|/files/ENCFF404EVY/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.92 and\
    \ a self consistency ratio of 2.46. 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.\n\n**audit\\_warning**: Replicate\
    \ concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible\
    \ Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF732BRI|/files/ENCFF732BRI/},\
    \ {ENCFF224KBA|/files/ENCFF224KBA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ have a rescue ratio of 1.92 and a self consistency ratio of 2.46. 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: ENCSR497VFH
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens K562
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002067/
    perturbed: false
    doi: 10.17989/ENCSR497VFH
    date_created: '2016-05-13T20:22:36.446229+00:00'
    date_released: '2018-01-26'
    submitter_comment: We note that this ChIP-seq experiment was performed using an
      antibody for which we have provided a compliant primary characterization but
      no secondary characterization.  A secondary characterization using IP-MS was
      attempted, but the experiment failed.  There is no remaining antibody from this
      lot number and therefore additional secondary characterizations cannot be attempted.
      However, because the replicate ChIP-seq datasets passed the ENCODE IDR ChIP-seq
      data quality standards, we are releasing the data to the public.
    target: ZNF639
