type: position_score
table:
  filename: ENCFF241UKW.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_ENCSR784VUY
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR784VUY [TISSUE: Homo sapiens H1, 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 {ENCAN022KVA|/analyses/ENCAN022KVA/} has in progress\
    \ subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: 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 {ENCFF561BFM|/files/ENCFF561BFM/}\
    \ processed by ChIP-seq ENCODE4 v1.7.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.39.\n\n**audit\\_not\\_compliant**: 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 {ENCFF561BFM|/files/ENCFF561BFM/}\
    \ processed by ChIP-seq ENCODE4 v1.7.1 GRCh38 pipeline was generated from a library\
    \ with PBC1 value of 0.34.\n\n**audit\\_warning**: Processed alignments file {ENCFF142ICR|/files/ENCFF142ICR/}\
    \ processed by ChIP-seq ENCODE4 v1.7.1 GRCh38 pipeline has 18428902 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ RNF2-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**:\
    \ Processed alignments file {ENCFF561BFM|/files/ENCFF561BFM/} processed by ChIP-seq\
    \ ENCODE4 v1.7.1 GRCh38 pipeline has 10731157 usable fragments. The minimum ENCODE\
    \ standard for each replicate in a ChIP-seq experiment targeting RNF2-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**: 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 {ENCFF561BFM|/files/ENCFF561BFM/} processed\
    \ by ChIP-seq ENCODE4 v1.7.1 GRCh38 pipeline was generated from a library with\
    \ PBC2 value of 1.37.\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 {ENCFF241UKW|/files/ENCFF241UKW/}\
    \ processed by ChIP-seq ENCODE4 v1.7.1 GRCh38 pipeline have a rescue ratio of\
    \ 1.63 and a self consistency ratio of 5.30. 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: ENCSR784VUY
    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/ENCSR784VUY
    date_created: '2016-02-26T02:58:26.093581+00:00'
    date_released: '2016-12-06'
    submitter_comment: PJF:For the RNF2 antibody, is this the same one that the Snyder
      lab validated using IP and mass spec?  Is the problem that it was validated
      for K562 and you have used it for hES?  If so, I would be supportive of releasing
      that data with the statement that the antibody was characterized in K562 cells
      using an IP-western as a primary and mass spec as a secondary characterization.
    target: RNF2