type: position_score
table:
  filename: ENCFF410RJD.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_ENCSR000EHH
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000EHH [biosample_summary="Homo sapiens K562" and target="NRF1"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000EHH [biosample_summary="Homo sapiens K562" and target="NRF1"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: IDR thresholded peaks\n\n**audit\\_error**:\
    \ Processed alignments file {ENCFF174DVW|/files/ENCFF174DVW/} processed by ChIP-seq\
    \ ENCODE4 v1.6.1 GRCh38 pipeline has 3624859 usable fragments. The minimum ENCODE\
    \ standard for each replicate in a ChIP-seq experiment targeting NRF1-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\\_internal\\_action**:\
    \ Released analysis {ENCAN390HVE|/analyses/ENCAN390HVE/} has in progress subobject\
    \ quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\n**audit\\\
    _internal\\_action**: Released analysis {ENCAN390HVE|/analyses/ENCAN390HVE/} has\
    \ in progress subobject document {6c5ccc37-b301-436c-b455-6178f2df7c51|/documents/6c5ccc37-b301-436c-b455-6178f2df7c51/}\n\
    \n**audit\\_warning**: Processed alignments file {ENCFF718OLQ|/files/ENCFF718OLQ/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 15385621 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ NRF1-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**:\
    \ PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of\
    \ genomic locations where exactly one read maps uniquely (M1) to the number of\
    \ genomic locations where two reads map uniquely (M2). A PBC2 value in the range\
    \ 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild\
    \ bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but\
    \ > 3 is acceptable. ENCODE processed alignments file {ENCFF718OLQ|/files/ENCFF718OLQ/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 9.94.\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 {ENCFF410RJD|/files/ENCFF410RJD/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of\
    \ 1.89 and a self consistency ratio of 5.87. 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: ENCSR000EHH
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens K562
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002067/
    perturbed: false
    doi: 10.17989/ENCSR000EHH
    date_created: '2014-02-12T23:17:56.501964+00:00'
    date_released: '2011-10-29'
    submitter_comment: ''
    target: NRF1