type: position_score
table:
  filename: ENCFF705TGT.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_ENCSR036KFJ
  column_index: 3
  type: float
  desc: 'Histone_ChIP-seq ENCSR036KFJ [biosample_summary="Homo sapiens Loucy" and target="H3K4me1"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'Histone_ChIP-seq ENCSR036KFJ [biosample_summary="Homo sapiens Loucy" and target="H3K4me1"]'
  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 {ENCAN128ZPT|/analyses/ENCAN128ZPT/} has in progress\
    \ subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN128ZPT|/analyses/ENCAN128ZPT/}\
    \ has in progress subobject document {8e60bb6f-23dc-4335-ae9a-fa656672a4b0|/documents/8e60bb6f-23dc-4335-ae9a-fa656672a4b0/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF009TIE|/files/ENCFF009TIE/}\
    \ processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 18823271 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3K4me1-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 {ENCFF147IFR|/files/ENCFF147IFR/}\
    \ processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 25430053 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3K4me1-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**: 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 {ENCFF009TIE|/files/ENCFF009TIE/}\
    \ processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.41.\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 {ENCFF009TIE|/files/ENCFF009TIE/}\
    \ processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library\
    \ with PBC1 value of 0.40.\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 {ENCFF009TIE|/files/ENCFF009TIE/} processed by ChIP-seq ENCODE4 v1.5.1\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 1.65.\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\
    \ {ENCFF147IFR|/files/ENCFF147IFR/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38\
    \ pipeline was generated from a library with PBC1 value of 0.90.\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 {ENCFF147IFR|/files/ENCFF147IFR/}\
    \ processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 9.70."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR036KFJ
    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/ENCSR036KFJ
    date_created: '2014-02-20T04:37:49.376876+00:00'
    date_released: '2014-09-04'
    submitter_comment: ''
    target: H3K4me1