type: position_score
table:
  filename: ENCFF574YMJ.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_ENCSR238QRG
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR238QRG [biosample_summary="Homo sapiens HepG2" and target="TBX3"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR238QRG [biosample_summary="Homo sapiens HepG2" and target="TBX3"]'
  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 {ENCAN264GQQ|/analyses/ENCAN264GQQ/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\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 {ENCFF274SQL|/files/ENCFF274SQL/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ was generated from a library with PBC1 value of 0.90.\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 {ENCFF274SQL|/files/ENCFF274SQL/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\
    \ PBC2 value of 9.81.\n\n**audit\\_warning**: Replicate concordance in ChIP-seq\
    \ experiments is measured by calculating IDR values (Irreproducible Discovery\
    \ Rate). ENCODE processed IDR thresholded peaks files {ENCFF574YMJ|/files/ENCFF574YMJ/},\
    \ {ENCFF852LYH|/files/ENCFF852LYH/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ have a rescue ratio of 1.80 and a self consistency ratio of 3.56. 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**: Replicate concordance in ChIP-seq experiments is measured\
    \ by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed\
    \ IDR thresholded peaks files {ENCFF312IIZ|/files/ENCFF312IIZ/}, {ENCFF580ZML|/files/ENCFF580ZML/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.80 and\
    \ a self consistency ratio of 3.56. 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."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR238QRG
    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/ENCSR238QRG
    date_created: '2016-05-13T00:09:16.462825+00:00'
    date_released: '2017-01-31'
    submitter_comment: Please note that the 'mixed platform' warning comes from the
      archived fastqs that were sequenced on the HiSeq2000 platform that if used,
      should be paired with the matching HiSeq2000 control ENCSR121CWV. The pipeline
      was run on the fastqs and controls sequenced on the HiSeq4000 platform for consistency.
    target: TBX3
