type: position_score
table:
  filename: ENCFF716JUM.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: ATAC-seq_ENCSR587TRP
  column_index: 3
  type: float
  desc: 'ATAC-seq ENCSR587TRP [biosample_summary="Homo sapiens SK-N-SH treated with 6 \u03BC\ M all-trans-retinoic acid for 48 hours"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR587TRP [biosample_summary="Homo sapiens SK-N-SH treated with 6 \u03BC\ M all-trans-retinoic acid for 48 hours"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2,\
    \ Rep 3\n\n**summary**: treated with 6 \u03BCM all-trans-retinoic acid for 48\
    \ hours\n\n**output\\_type**: pseudoreplicated peaks\n\n**audit\\_internal\\_action**:\
    \ Released analysis {ENCAN752KCW|/analyses/ENCAN752KCW/} has in progress subobject\
    \ quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}\n\n\
    **audit\\_internal\\_action**: Released analysis {ENCAN752KCW|/analyses/ENCAN752KCW/}\
    \ has in progress subobject document {4b73c5ee-3525-4422-85bb-2df42d4f53a6|/documents/4b73c5ee-3525-4422-85bb-2df42d4f53a6/}\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 < 0.7 is poor complexity, between 0.7 and 0.9 is moderate\
    \ complexity, and >= 0.9 high complexity. NRF value > 0.9 is recommended, but\
    \ > 0.7 is acceptable. ENCODE processed file {ENCFF049RWL|/files/ENCFF049RWL/}\
    \ processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.874478.\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 > 0.7 is\
    \ acceptable. ENCODE processed file {ENCFF049RWL|/files/ENCFF049RWL/} processed\
    \ by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with\
    \ a PBC1 value of 0.88.\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 < 0.7 is poor complexity,\
    \ between 0.7 and 0.9 is moderate complexity, and >= 0.9 high complexity. NRF\
    \ value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF270AGJ|/files/ENCFF270AGJ/}\
    \ processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.874897.\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 > 0.7 is\
    \ acceptable. ENCODE processed file {ENCFF270AGJ|/files/ENCFF270AGJ/} processed\
    \ by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with\
    \ a PBC1 value of 0.88.\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 < 0.7 is poor complexity,\
    \ between 0.7 and 0.9 is moderate complexity, and >= 0.9 high complexity. NRF\
    \ value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF502IYP|/files/ENCFF502IYP/}\
    \ processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.870587.\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 > 0.7 is\
    \ acceptable. ENCODE processed file {ENCFF502IYP|/files/ENCFF502IYP/} processed\
    \ by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with\
    \ a PBC1 value of 0.88."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR587TRP
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: "treated with 6 \u03BCM all-trans-retinoic acid for\
      \ 48 hours"
    biosample_summary: "Homo sapiens SK-N-SH treated with 6 \u03BCM all-trans-retinoic\
      \ acid for 48 hours"
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0003072/
    perturbed: false
    doi: 10.17989/ENCSR587TRP
    date_created: '2019-07-30T08:28:26.975990+00:00'
    date_released: '2020-08-05'
    submitter_comment: ''