type: position_score
table:
  filename: ENCFF539MIO.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_ENCSR000ATM
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000ATM [biosample_summary="Homo sapiens K562" and target="REST"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000ATM [biosample_summary="Homo sapiens K562" and target="REST"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2,\
    \ Rep 3\n\n**summary**: \n\n**output\\_type**: IDR thresholded peaks\n\n**audit\\\
    _internal\\_action**: Released analysis {ENCAN583YOZ|/analyses/ENCAN583YOZ/} has\
    \ in progress subobject document {2166f896-7932-4999-aa61-9723afbfa3a9|/documents/2166f896-7932-4999-aa61-9723afbfa3a9/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN583YOZ|/analyses/ENCAN583YOZ/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF191OSK|/files/ENCFF191OSK/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 7468228 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ REST-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\\_not\\\
    _compliant**: Processed alignments file {ENCFF565CHM|/files/ENCFF565CHM/} processed\
    \ by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 8956380 usable fragments. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ REST-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\\_not\\\
    _compliant**: NRF (Non Redundant Fraction) is equal to the result of the division\
    \ of the number of reads after duplicates removal by the total number of reads.\
    \ An NRF value in the range 0 - 0.5 is poor complexity, 0.5 - 0.8 is moderate\
    \ complexity, and > 0.8 high complexity. NRF value > 0.8 is recommended, but >\
    \ 0.5 is acceptable. ENCODE processed alignments file {ENCFF191OSK|/files/ENCFF191OSK/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.23.\n\n**audit\\_not\\_compliant**: PBC1 (PCR Bottlenecking\
    \ Coefficient 1, M1/M\\_distinct) is the ratio of the number of genomic locations\
    \ where exactly one read maps uniquely (M1) to the number of genomic locations\
    \ where some reads map (M\\_distinct). A PBC1 value in the range 0 - 0.5 is severe\
    \ bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking,\
    \ and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.8 is\
    \ acceptable. ENCODE processed alignments file {ENCFF191OSK|/files/ENCFF191OSK/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC1 value of 0.22.\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 {ENCFF191OSK|/files/ENCFF191OSK/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 1.41.\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 {ENCFF539MIO|/files/ENCFF539MIO/} processed by ChIP-seq ENCODE4\
    \ v1.6.1 GRCh38 pipeline have a rescue ratio of 1.12 and a self consistency ratio\
    \ of 4.91. 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: ENCSR000ATM
    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/ENCSR000ATM
    date_created: '2013-11-07T22:16:29.359993+00:00'
    date_released: '2012-08-06'
    submitter_comment: ''
    target: REST