type: position_score
table:
  filename: ENCFF627DJP.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_ENCSR000DOI
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000DOI [biosample_summary="Homo sapiens K562" and target="POLR3A"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000DOI [biosample_summary="Homo sapiens K562" and target="POLR3A"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: IDR thresholded peaks\n\n**audit\\_error**:\
    \ Processed alignments file {ENCFF752EDG|/files/ENCFF752EDG/} processed by ChIP-seq\
    \ ENCODE4 v1.6.1 GRCh38 pipeline has 3909840 usable fragments. The minimum ENCODE\
    \ standard for each replicate in a ChIP-seq experiment targeting POLR3A-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\\_internal\\\
    _action**: Released analysis {ENCAN794VLL|/analyses/ENCAN794VLL/} has in progress\
    \ subobject document {f2989020-7946-4961-85e7-af5c88398620|/documents/f2989020-7946-4961-85e7-af5c88398620/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN794VLL|/analyses/ENCAN794VLL/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF888ZBM|/files/ENCFF888ZBM/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 5002721 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ POLR3A-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**: 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 {ENCFF752EDG|/files/ENCFF752EDG/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.78.\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 {ENCFF752EDG|/files/ENCFF752EDG/} processed\
    \ by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with\
    \ PBC1 value of 0.88.\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 {ENCFF627DJP|/files/ENCFF627DJP/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of\
    \ 1.52 and a self consistency ratio of 2.39. 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: ENCSR000DOI
    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/ENCSR000DOI
    date_created: '2014-02-12T23:29:24.354002+00:00'
    date_released: '2011-10-29'
    submitter_comment: ''
    target: POLR3A
