type: position_score
table:
  filename: ENCFF985QBS.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_ENCSR000ATL
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000ATL [biosample_summary="Homo sapiens K562" and target="CHD4"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000ATL [biosample_summary="Homo sapiens K562" and target="CHD4"]'
  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 {ENCAN976BUX|/analyses/ENCAN976BUX/} has\
    \ in progress subobject document {3a79b486-618a-4a86-9fab-337c28c39da1|/documents/3a79b486-618a-4a86-9fab-337c28c39da1/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN976BUX|/analyses/ENCAN976BUX/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF871KJZ|/files/ENCFF871KJZ/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 5438385 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ CHD4-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 {ENCFF871KJZ|/files/ENCFF871KJZ/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.26.\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 {ENCFF871KJZ|/files/ENCFF871KJZ/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC1 value of 0.20.\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 {ENCFF985QBS|/files/ENCFF985QBS/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of\
    \ 3.34 and a self consistency ratio of 194.39. 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 {ENCFF073KUJ|/files/ENCFF073KUJ/} processed by ChIP-seq\
    \ ENCODE4 v1.6.1 GRCh38 pipeline has 11936786 usable fragments. The minimum ENCODE\
    \ standard for each replicate in a ChIP-seq experiment targeting CHD4-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 {ENCFF871KJZ|/files/ENCFF871KJZ/} processed\
    \ by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with\
    \ PBC2 value of 1.20."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000ATL
    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/ENCSR000ATL
    date_created: '2013-11-07T22:16:06.487429+00:00'
    date_released: '2012-08-06'
    submitter_comment: ''
    target: CHD4