type: position_score
table:
  filename: ENCFF451AII.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_ENCSR000DYR
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000DYR [biosample_summary="Homo sapiens GM12878" and target="CUX1"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000DYR [biosample_summary="Homo sapiens GM12878" and target="CUX1"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: IDR thresholded peaks\n\n**audit\\_internal\\\
    _action**: Released analysis {ENCAN456KNT|/analyses/ENCAN456KNT/} has in progress\
    \ subobject document {a657444c-1608-4400-af57-5c3c53baadcd|/documents/a657444c-1608-4400-af57-5c3c53baadcd/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN456KNT|/analyses/ENCAN456KNT/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-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 {ENCFF451AII|/files/ENCFF451AII/} processed by ChIP-seq\
    \ ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 7.10 and a self consistency\
    \ ratio of 4.34. 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\
    \ {ENCFF040UPE|/files/ENCFF040UPE/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38\
    \ pipeline has 14791165 usable fragments. The minimum ENCODE standard for each\
    \ replicate in a ChIP-seq experiment targeting CUX1-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: ENCSR000DYR
    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/ENCSR000DYR
    date_created: '2014-02-12T22:55:35.404554+00:00'
    date_released: '2012-08-20'
    submitter_comment: ''
    target: CUX1
