type: position_score
table:
  filename: ENCFF712JXT.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_ENCSR000DKT
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000DKT [biosample_summary="Homo sapiens GM12878" and target="POLR2A"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000DKT [biosample_summary="Homo sapiens GM12878" and target="POLR2A"]'
  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 {ENCAN661YRX|/analyses/ENCAN661YRX/} has in progress\
    \ subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN661YRX|/analyses/ENCAN661YRX/}\
    \ has in progress subobject document {61409001-0c92-4c03-b570-6f833ad65e2b|/documents/61409001-0c92-4c03-b570-6f833ad65e2b/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF355JUH|/files/ENCFF355JUH/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 7416641 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ POLR2A-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\\\
    _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 {ENCFF355JUH|/files/ENCFF355JUH/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.48.\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 {ENCFF355JUH|/files/ENCFF355JUH/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC1 value of 0.46.\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 {ENCFF712JXT|/files/ENCFF712JXT/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of\
    \ 3.25 and a self consistency ratio of 49.97. 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 {ENCFF424XHE|/files/ENCFF424XHE/} processed by ChIP-seq\
    \ ENCODE4 v1.6.1 GRCh38 pipeline has 12595144 usable fragments. The minimum ENCODE\
    \ standard for each replicate in a ChIP-seq experiment targeting POLR2A-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 {ENCFF355JUH|/files/ENCFF355JUH/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 1.72.\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 {ENCFF424XHE|/files/ENCFF424XHE/} processed\
    \ by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with\
    \ PBC1 value of 0.90."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000DKT
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens GM12878
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002784/
    perturbed: false
    doi: 10.17989/ENCSR000DKT
    date_created: '2013-09-13T16:01:12.930220-08:00'
    date_released: '2011-03-17'
    submitter_comment: ''
    target: POLR2A
