type: position_score
table:
  filename: ENCFF964JXI.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_ENCSR000BHU
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000BHU [biosample_summary="Homo sapiens HepG2" and target="RXRA"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000BHU [biosample_summary="Homo sapiens HepG2" and target="RXRA"]'
  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 {ENCAN964FSC|/analyses/ENCAN964FSC/} 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 {ENCFF799DNN|/files/ENCFF799DNN/}, {ENCFF964JXI|/files/ENCFF964JXI/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 2.11 and\
    \ a self consistency ratio of 5.72. 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 {ENCFF145AUL|/files/ENCFF145AUL/}, {ENCFF071UJQ|/files/ENCFF071UJQ/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 2.11 and a self consistency\
    \ ratio of 5.72. 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\
    \ {ENCFF881TVG|/files/ENCFF881TVG/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ has 10305695 usable fragments. The minimum ENCODE standard for each replicate\
    \ in a ChIP-seq experiment targeting RXRA-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**: 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 {ENCFF881TVG|/files/ENCFF881TVG/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ was generated from a library with PBC1 value of 0.84.\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 {ENCFF881TVG|/files/ENCFF881TVG/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\
    \ PBC2 value of 6.23."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000BHU
    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/ENCSR000BHU
    date_created: '2013-09-13T15:57:41.670293-08:00'
    date_released: '2011-07-18'
    submitter_comment: ''
    target: RXRA