type: position_score
table:
  filename: ENCFF516NJV.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: Histone_ChIP-seq_ENCSR678AFU
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR678AFU [TISSUE: Homo sapiens OCI-LY1, TARGET: H3F3A]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: pseudoreplicated peaks\n\n**audit\\_internal\\\
    _action**: Released analysis {ENCAN048UON|/analyses/ENCAN048UON/} has in progress\
    \ subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN048UON|/analyses/ENCAN048UON/}\
    \ has in progress subobject document {532f7eef-158d-489a-b10f-0795b4d78830|/documents/532f7eef-158d-489a-b10f-0795b4d78830/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF095TUA|/files/ENCFF095TUA/}\
    \ processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline has 22348397 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3F3A-human and investigated as a broad histone mark is 20 million usable fragments.\
    \ The recommended value is > 45 million, but > 35 million is acceptable. (See\
    \ {ENCODE ChIP-seq data standards|/data-standards/chip-seq/})\n\n**audit\\_not\\\
    _compliant**: Processed alignments file {ENCFF499IEY|/files/ENCFF499IEY/} processed\
    \ by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline has 23698035 usable fragments. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3F3A-human and investigated as a broad histone mark is 20 million usable fragments.\
    \ The recommended value is > 45 million, but > 35 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 {ENCFF095TUA|/files/ENCFF095TUA/} processed\
    \ by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library with\
    \ NRF value of 0.61.\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 {ENCFF095TUA|/files/ENCFF095TUA/} processed\
    \ by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library with\
    \ PBC1 value of 0.58.\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 {ENCFF095TUA|/files/ENCFF095TUA/} processed by ChIP-seq ENCODE4 v1.6.0\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 2.25.\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 {ENCFF499IEY|/files/ENCFF499IEY/}\
    \ processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.63.\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 {ENCFF499IEY|/files/ENCFF499IEY/} processed\
    \ by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library with\
    \ PBC1 value of 0.61.\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 {ENCFF499IEY|/files/ENCFF499IEY/} processed by ChIP-seq ENCODE4 v1.6.0\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 2.35."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR678AFU
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens OCI-LY1
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0005907/
    perturbed: false
    doi: 10.17989/ENCSR678AFU
    date_created: '2014-02-26T22:12:43.952169+00:00'
    date_released: '2014-07-11'
    submitter_comment: ''
    target: H3F3A
