type: position_score
table:
  filename: ENCFF177YDT.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_ENCSR000BNT
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR000BNT [TISSUE: Homo sapiens HepG2, TARGET: YY1]'
  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 {ENCAN610LOW|/analyses/ENCAN610LOW/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_internal\\_action**: File {ENCFF177YDT|/files/ENCFF177YDT/} with status\
    \ 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status\
    \ 'archived'.\n\n**audit\\_not\\_compliant**: Processed alignments file {ENCFF056BXB|/files/ENCFF056BXB/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 8791741 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ YY1-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**: Replicate concordance in ChIP-seq experiments is measured by calculating\
    \ IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded\
    \ peaks files {ENCFF954VXQ|/files/ENCFF954VXQ/}, {ENCFF520IPU|/files/ENCFF520IPU/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 2.40 and\
    \ a self consistency ratio of 2.38. 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 {ENCFF042DUJ|/files/ENCFF042DUJ/}, {ENCFF177YDT|/files/ENCFF177YDT/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 2.40 and a self consistency\
    \ ratio of 2.38. 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\
    \ {ENCFF499BAH|/files/ENCFF499BAH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ has 13941122 usable fragments. The minimum ENCODE standard for each replicate\
    \ in a ChIP-seq experiment targeting YY1-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**: 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 {ENCFF056BXB|/files/ENCFF056BXB/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ NRF value of 0.52.\n\n**audit\\_warning**: 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 {ENCFF056BXB|/files/ENCFF056BXB/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value\
    \ of 0.51.\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 {ENCFF056BXB|/files/ENCFF056BXB/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC2 value of 1.84."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000BNT
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens HepG2
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0001187/
    perturbed: false
    doi: 10.17989/ENCSR000BNT
    date_created: '2013-09-13T16:02:10.464011-08:00'
    date_released: '2011-07-18'
    submitter_comment: ''
    target: YY1