type: position_score
table:
  filename: ENCFF855GTI.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_ENCSR000DVG
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR000DVG [TISSUE: Homo sapiens kidney epithelial cell, TARGET:
    H3K4me3]'
  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 {ENCAN644AAA|/analyses/ENCAN644AAA/} has in progress\
    \ subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN644AAA|/analyses/ENCAN644AAA/}\
    \ has in progress subobject document {21e57bec-6d47-4f03-aef6-0e2d81f72313|/documents/21e57bec-6d47-4f03-aef6-0e2d81f72313/}\n\
    \n**audit\\_warning**: Processed alignments file {ENCFF222GZJ|/files/ENCFF222GZJ/}\
    \ processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 10742571 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3K4me3-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**: Processed alignments file {ENCFF925WTZ|/files/ENCFF925WTZ/} processed\
    \ by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 12081735 usable fragments. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3K4me3-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**: 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\
    \ {ENCFF222GZJ|/files/ENCFF222GZJ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38\
    \ pipeline was generated from a library with PBC1 value of 0.86.\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 {ENCFF222GZJ|/files/ENCFF222GZJ/}\
    \ processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 7.55.\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 {ENCFF925WTZ|/files/ENCFF925WTZ/} processed\
    \ by ChIP-seq ENCODE4 v1.5.1 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 {ENCFF925WTZ|/files/ENCFF925WTZ/} processed by ChIP-seq ENCODE4 v1.5.1\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 8.17."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000DVG
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens kidney epithelial cell
    replication_type: isogenic
    biosample_ontology: /biosample-types/primary_cell_CL_0002518/
    perturbed: false
    doi: 10.17989/ENCSR000DVG
    date_created: '2014-02-12T22:40:47.412521+00:00'
    date_released: '2011-02-11'
    submitter_comment: Replicate 2,1 of this experiment was previously attributed
      to biosample ENCBS056ENC and replicate 1,1 of this experiment was previously
      attributed to biosample ENCBS056ENC but they have since been corrected to the
      current biosamples. Please note that the biosample term has remain unchanged.
    target: H3K4me3
