type: position_score
table:
  filename: ENCFF507XOB.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_ENCSR000AUC
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000AUC [biosample_summary="Homo sapiens K562" and target="SUZ12"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000AUC [biosample_summary="Homo sapiens K562" and target="SUZ12"]'
  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**: Archived analysis {ENCAN197AQC|/analyses/ENCAN197AQC/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF062OKC|/files/ENCFF062OKC/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline has 6341123 usable fragments. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ SUZ12-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 {ENCFF062OKC|/files/ENCFF062OKC/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\
    \ NRF value of 0.39.\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 {ENCFF062OKC|/files/ENCFF062OKC/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value\
    \ of 0.38.\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 {ENCFF507XOB|/files/ENCFF507XOB/}, {ENCFF019XTP|/files/ENCFF019XTP/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 3.18 and\
    \ a self consistency ratio of 12.76. 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\\_not\\_compliant**:\
    \ Replicate concordance in ChIP-seq experiments is measured by calculating IDR\
    \ values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks\
    \ files {ENCFF757GUM|/files/ENCFF757GUM/}, {ENCFF385HPA|/files/ENCFF385HPA/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 3.18 and a self consistency\
    \ ratio of 12.76. 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**: 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 {ENCFF062OKC|/files/ENCFF062OKC/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ was generated from a library with PBC2 value of 1.73."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000AUC
    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/ENCSR000AUC
    date_created: '2013-11-07T22:16:24.512277+00:00'
    date_released: '2012-08-06'
    submitter_comment: As of June 8th 2018, this experiment has been run through the
      uniform processing pipeline for both assemblies.
    target: SUZ12