type: position_score
table:
  filename: ENCFF617RGJ.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_ENCSR000AQK
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR000AQK [TISSUE: Homo sapiens H1, TARGET: CHD1]'
  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 {ENCAN020HYO|/analyses/ENCAN020HYO/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\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 {ENCFF617RGJ|/files/ENCFF617RGJ/}, {ENCFF693GHB|/files/ENCFF693GHB/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 2.47 and\
    \ a self consistency ratio of 6.00. 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 {ENCFF741MOG|/files/ENCFF741MOG/}, {ENCFF735ZAF|/files/ENCFF735ZAF/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 2.47 and a self consistency\
    \ ratio of 6.00. 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**: 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 {ENCFF847WER|/files/ENCFF847WER/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value\
    \ of 0.82.\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 {ENCFF847WER|/files/ENCFF847WER/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ was generated from a library with PBC2 value of 5.81."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000AQK
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens H1
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0003042/
    perturbed: false
    doi: 10.17989/ENCSR000AQK
    date_created: '2013-11-07T22:16:16.669903+00:00'
    date_released: '2012-03-06'
    submitter_comment: As of February 28, 2017, new mapping and peak calling is required
      due to duplicated files.
    target: CHD1
