type: position_score
table:
  filename: ENCFF005JKU.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_ENCSR000DZS
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000DZS [biosample_summary="Homo sapiens GM12878" and target="BRCA1"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000DZS [biosample_summary="Homo sapiens GM12878" and target="BRCA1"]'
  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 {ENCFF005JKU|/files/ENCFF005JKU/} with status 'released'\
    \ is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'.\n\
    \n**audit\\_internal\\_action**: Archived analysis {ENCAN432HAZ|/analyses/ENCAN432HAZ/}\
    \ has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_warning**: Processed alignments file {ENCFF651OUX|/files/ENCFF651OUX/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 14261745 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ BRCA1-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 {ENCFF365KGA|/files/ENCFF365KGA/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline has 18898081 usable fragments. The minimum\
    \ ENCODE standard for each replicate in a ChIP-seq experiment targeting BRCA1-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 {ENCFF003ZGU|/files/ENCFF003ZGU/}, {ENCFF005JKU|/files/ENCFF005JKU/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 3.34 and a self consistency\
    \ ratio of 1.84. 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 {ENCFF794VJN|/files/ENCFF794VJN/},\
    \ {ENCFF616FBI|/files/ENCFF616FBI/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ have a rescue ratio of 3.34 and a self consistency ratio of 1.84. 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: ENCSR000DZS
    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/ENCSR000DZS
    date_created: '2014-02-12T23:21:18.924782+00:00'
    date_released: '2011-10-29'
    submitter_comment: ''
    target: BRCA1