type: position_score
table:
  filename: ENCFF712GLE.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_ENCSR000DZR
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000DZR [biosample_summary="Homo sapiens GM12878" and target="CHD2"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000DZR [biosample_summary="Homo sapiens GM12878" and target="CHD2"]'
  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**: Archived analysis {ENCAN547TAA|/analyses/ENCAN547TAA/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Replicate concordance in ChIP-seq experiments is\
    \ measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed\
    \ IDR thresholded peaks files {ENCFF848RCO|/files/ENCFF848RCO/} processed by ChIP-seq\
    \ ENCODE3 hg19 pipeline have a rescue ratio of 2.13 and a self consistency ratio\
    \ of 2.23. 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\\_not\\_compliant**: Replicate concordance in ChIP-seq\
    \ experiments is measured by calculating IDR values (Irreproducible Discovery\
    \ Rate). ENCODE processed IDR thresholded peaks files {ENCFF712GLE|/files/ENCFF712GLE/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 2.13 and\
    \ a self consistency ratio of 2.23. 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**: Processed\
    \ alignments file {ENCFF760ZDH|/files/ENCFF760ZDH/} processed by ChIP-seq ENCODE3\
    \ hg19 pipeline has 12857161 usable fragments. The minimum ENCODE standard for\
    \ each replicate in a ChIP-seq experiment targeting CHD2-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**: Processed alignments\
    \ file {ENCFF450UXL|/files/ENCFF450UXL/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ has 16726958 usable fragments. The minimum ENCODE standard for each replicate\
    \ in a ChIP-seq experiment targeting CHD2-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/}\
    \ )"
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000DZR
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens GM12878
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002784/
    perturbed: false
    doi: 10.17989/ENCSR000DZR
    date_created: '2014-02-12T23:21:16.241624+00:00'
    date_released: '2011-10-29'
    submitter_comment: ''
    target: CHD2
