type: position_score
table:
  filename: ENCFF963VBZ.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: TF_ChIP-seq_ENCSR969AIM
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: "ChIP-seq ENCSR969AIM [TISSUE: Homo sapiens SK-N-SH genetically modified\
    \ (insertion) using CRISPR targeting H. sapiens PATZ1 treated with 6 \u03BCM all-trans-retinoic\
    \ acid for 48 hours, TARGET: PATZ1]"
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: treated with 6 \u03BCM all-trans-retinoic acid for 48 hours genetically\
    \ modified (insertion) using CRISPR targeting H. sapiens PATZ1\n\n**output\\_type**:\
    \ IDR thresholded peaks\n\n**audit\\_internal\\_action**: Released analysis {ENCAN034YZU|/analyses/ENCAN034YZU/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\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 {ENCFF463JPM|/files/ENCFF463JPM/}\
    \ processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.67.\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 {ENCFF463JPM|/files/ENCFF463JPM/} processed\
    \ by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with\
    \ PBC1 value of 0.68.\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 {ENCFF463JPM|/files/ENCFF463JPM/} processed by ChIP-seq ENCODE4 v1.8.0\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 3.15.\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 {ENCFF617DAJ|/files/ENCFF617DAJ/}\
    \ processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.60.\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 {ENCFF617DAJ|/files/ENCFF617DAJ/} processed\
    \ by ChIP-seq ENCODE4 v1.8.0 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 {ENCFF617DAJ|/files/ENCFF617DAJ/} processed by ChIP-seq ENCODE4 v1.8.0\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 2.61.\n\n**audit\\\
    _warning**: Replicate concordance in ChIP-seq experiments is measured by calculating\
    \ IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded\
    \ peaks files {ENCFF963VBZ|/files/ENCFF963VBZ/} processed by ChIP-seq ENCODE4\
    \ v1.8.0 GRCh38 pipeline have a rescue ratio of 1.49 and a self consistency ratio\
    \ of 2.51. According to ENCODE standards, having both rescue ratio and self consistency\
    \ ratio values < 2 is recommended, but having only one of the ratio values < 2\
    \ is acceptable."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR969AIM
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: "treated with 6 \u03BCM all-trans-retinoic acid for\
      \ 48 hours genetically modified (insertion) using CRISPR targeting H. sapiens\
      \ PATZ1"
    biosample_summary: "Homo sapiens SK-N-SH genetically modified (insertion) using\
      \ CRISPR targeting H. sapiens PATZ1 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/ENCSR969AIM
    date_created: '2018-12-18T22:56:08.182518+00:00'
    date_released: '2020-07-14'
    submitter_comment: ''
    target: PATZ1