type: position_score
table:
  filename: ENCFF896UZB.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_ENCSR000DZZ
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000DZZ [biosample_summary="Homo sapiens GM12878" and target="TBP"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000DZZ [biosample_summary="Homo sapiens GM12878" and target="TBP"]'
  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 {ENCFF896UZB|/files/ENCFF896UZB/} with status 'released'\
    \ is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'.\n\
    \n**audit\\_internal\\_action**: Archived analysis {ENCAN195QRQ|/analyses/ENCAN195QRQ/}\
    \ has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_warning**: Processed alignments file {ENCFF987AWV|/files/ENCFF987AWV/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 15331321 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ TBP-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 {ENCFF910NHM|/files/ENCFF910NHM/} processed by ChIP-seq\
    \ ENCODE3 GRCh38 pipeline has 15105795 usable fragments. The minimum ENCODE standard\
    \ for each replicate in a ChIP-seq experiment targeting TBP-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 {ENCFF571FGG|/files/ENCFF571FGG/},\
    \ {ENCFF896UZB|/files/ENCFF896UZB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ have a rescue ratio of 1.31 and a self consistency ratio of 9.71. 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 {ENCFF268NXQ|/files/ENCFF268NXQ/}, {ENCFF383GJE|/files/ENCFF383GJE/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.31 and\
    \ a self consistency ratio of 9.71. 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: ENCSR000DZZ
    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/ENCSR000DZZ
    date_created: '2014-02-12T23:05:16.070282+00:00'
    date_released: '2011-10-29'
    submitter_comment: ''
    target: TBP
