type: position_score
table:
  filename: ENCFF409SDU.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_ENCSR138FUZ
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR138FUZ [biosample_summary="Homo sapiens K562" and target="RNF2"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR138FUZ [biosample_summary="Homo sapiens K562" and target="RNF2"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: IDR thresholded peaks\n\n**audit\\_internal\\\
    _action**: Released analysis {ENCAN062GAH|/analyses/ENCAN062GAH/} has in progress\
    \ subobject document {1b7dfe79-5aa8-485f-8f0c-df199e7c4a5c|/documents/1b7dfe79-5aa8-485f-8f0c-df199e7c4a5c/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN062GAH|/analyses/ENCAN062GAH/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-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 {ENCFF285FVC|/files/ENCFF285FVC/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with PBC1 value of 0.85.\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 {ENCFF285FVC|/files/ENCFF285FVC/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 6.64.\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 {ENCFF409SDU|/files/ENCFF409SDU/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of\
    \ 1.53 and a self consistency ratio of 4.22. 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: ENCSR138FUZ
    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/ENCSR138FUZ
    date_created: '2014-07-02T22:39:08.385586+00:00'
    date_released: '2014-07-07'
    submitter_comment: ''
    target: RNF2