type: position_score
table:
  filename: ENCFF997VAB.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_ENCSR000BJI
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR000BJI [TISSUE: Homo sapiens GM12892, TARGET: PAX5]'
  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 {ENCAN775KQJ|/analyses/ENCAN775KQJ/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_internal\\_action**: File {ENCFF997VAB|/files/ENCFF997VAB/} with status\
    \ 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status\
    \ 'archived'.\n\n**audit\\_not\\_compliant**: Processed alignments file {ENCFF968WVT|/files/ENCFF968WVT/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 8173942 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ PAX5-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**: Processed alignments file {ENCFF853EOZ|/files/ENCFF853EOZ/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline has 5031895 usable fragments. The minimum\
    \ ENCODE standard for each replicate in a ChIP-seq experiment targeting PAX5-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 {ENCFF853EOZ|/files/ENCFF853EOZ/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with NRF value\
    \ of 0.35.\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 {ENCFF853EOZ|/files/ENCFF853EOZ/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value\
    \ of 0.25.\n\n**audit\\_not\\_compliant**: 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 {ENCFF853EOZ|/files/ENCFF853EOZ/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC2 value of 0.96.\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 {ENCFF009EFA|/files/ENCFF009EFA/}, {ENCFF466ZRQ|/files/ENCFF466ZRQ/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 2.87 and\
    \ a self consistency ratio of 5.92. 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\\_not\\_compliant**:\
    \ Replicate concordance in ChIP-seq experiments is measured by calculating IDR\
    \ values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks\
    \ files {ENCFF300QIO|/files/ENCFF300QIO/}, {ENCFF997VAB|/files/ENCFF997VAB/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 2.87 and a self consistency\
    \ ratio of 5.92. 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**: 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 {ENCFF968WVT|/files/ENCFF968WVT/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with NRF value of 0.80.\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\
    \ {ENCFF968WVT|/files/ENCFF968WVT/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ was generated from a library with PBC1 value of 0.80.\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 {ENCFF968WVT|/files/ENCFF968WVT/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ PBC2 value of 4.91."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000BJI
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens GM12892
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002786/
    perturbed: false
    doi: 10.17989/ENCSR000BJI
    date_created: '2013-09-13T15:59:18.459484-08:00'
    date_released: '2011-07-18'
    submitter_comment: ''
    target: PAX5