type: position_score
table:
  filename: ENCFF271RGE.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_ENCSR000EUU
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR000EUU [TISSUE: Homo sapiens HCT116, TARGET: POLR2A]'
  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 {ENCFF271RGE|/files/ENCFF271RGE/} with status 'released'\
    \ is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'.\n\
    \n**audit\\_internal\\_action**: Archived analysis {ENCAN769JJJ|/analyses/ENCAN769JJJ/}\
    \ has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_error**: Processed alignments file {ENCFF339ZRD|/files/ENCFF339ZRD/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 4225138 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ POLR2A-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\\\
    _not\\_compliant**: Processed alignments file {ENCFF876UIJ|/files/ENCFF876UIJ/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 7235645 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ POLR2A-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 {ENCFF271RGE|/files/ENCFF271RGE/}, {ENCFF786BQV|/files/ENCFF786BQV/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.08 and\
    \ a self consistency ratio of 4.61. 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 {ENCFF804JZT|/files/ENCFF804JZT/},\
    \ {ENCFF192GSD|/files/ENCFF192GSD/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ have a rescue ratio of 1.08 and a self consistency ratio of 4.61. 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: ENCSR000EUU
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens HCT116
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002824/
    perturbed: false
    doi: 10.17989/ENCSR000EUU
    date_created: '2013-12-19T23:51:13.003519+00:00'
    date_released: '2011-10-29'
    submitter_comment: The data quality is too poor for peak analysis for hg19. Not
      enough peaks can be called. The GRCh38 data should also be used with caution.
    target: POLR2A
