type: position_score
table:
  filename: ENCFF656YRA.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_ENCSR165LOF
  column_index: 3
  type: float
  desc: 'Histone_ChIP-seq ENCSR165LOF [biosample_summary="Homo sapiens Loucy" and target="H3K4me2"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'Histone_ChIP-seq ENCSR165LOF [biosample_summary="Homo sapiens Loucy" and target="H3K4me2"]'
  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 {ENCAN637XPI|/analyses/ENCAN637XPI/} has in progress\
    \ subobject document {060a1797-608c-45b1-afd9-1d5ef89c0079|/documents/060a1797-608c-45b1-afd9-1d5ef89c0079/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN637XPI|/analyses/ENCAN637XPI/}\
    \ has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/}\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 {ENCFF281RMV|/files/ENCFF281RMV/}\
    \ processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.47.\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 {ENCFF281RMV|/files/ENCFF281RMV/}\
    \ processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library\
    \ with PBC1 value of 0.45.\n\n**audit\\_warning**: Processed alignments file {ENCFF281RMV|/files/ENCFF281RMV/}\
    \ processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline has 19683664 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3K4me2-human and investigated as a narrow histone mark 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 {ENCFF281RMV|/files/ENCFF281RMV/}\
    \ processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 1.79.\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 {ENCFF147IBW|/files/ENCFF147IBW/} processed\
    \ by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library with\
    \ PBC1 value of 0.87.\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 {ENCFF147IBW|/files/ENCFF147IBW/} processed by ChIP-seq ENCODE4 v1.6.0\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 7.37."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR165LOF
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens Loucy
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0007112/
    perturbed: false
    doi: 10.17989/ENCSR165LOF
    date_created: '2014-02-20T05:41:40.569231+00:00'
    date_released: '2014-09-04'
    submitter_comment: ''
    target: H3K4me2