type: position_score
table:
  filename: ENCFF444NKK.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_ENCSR000BJH
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR000BJH [TISSUE: Homo sapiens GM12891, TARGET: PAX5]'
  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 {ENCAN369XUF|/analyses/ENCAN369XUF/} has in progress\
    \ subobject document {ce9d5340-a2d2-4c35-b847-62e291848a2a|/documents/ce9d5340-a2d2-4c35-b847-62e291848a2a/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN369XUF|/analyses/ENCAN369XUF/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF614UWP|/files/ENCFF614UWP/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 7271012 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 {ENCFF579ZBC|/files/ENCFF579ZBC/} processed\
    \ by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 7153307 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**: 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\
    \ {ENCFF579ZBC|/files/ENCFF579ZBC/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38\
    \ pipeline was generated from a library with PBC1 value of 0.49.\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 {ENCFF614UWP|/files/ENCFF614UWP/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.54.\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 {ENCFF614UWP|/files/ENCFF614UWP/} processed\
    \ by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with\
    \ PBC1 value of 0.54.\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 {ENCFF614UWP|/files/ENCFF614UWP/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 1.94.\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 {ENCFF579ZBC|/files/ENCFF579ZBC/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.54.\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 {ENCFF579ZBC|/files/ENCFF579ZBC/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 1.73."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000BJH
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens GM12891
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002785/
    perturbed: false
    doi: 10.17989/ENCSR000BJH
    date_created: '2013-09-13T15:59:17.883234-08:00'
    date_released: '2011-07-18'
    submitter_comment: ''
    target: PAX5