type: position_score
table:
  filename: ENCFF834LQR.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_ENCSR634ZGP
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR634ZGP [TISSUE: Homo sapiens HeLa-S3, TARGET: UBTF]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: optimal IDR thresholded peaks\n\n**audit\\\
    _internal\\_action**: Archived analysis {ENCAN774VQB|/analyses/ENCAN774VQB/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_internal\\_action**: File {ENCFF834LQR|/files/ENCFF834LQR/} with status\
    \ 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status\
    \ 'archived'.\n\n**audit\\_internal\\_action**: Released file {ENCFF834LQR|/files/ENCFF834LQR/}\
    \ has replaced subobject file {c4c4d92c-b35a-4c43-9b66-bf5d92f8641d|/files/c4c4d92c-b35a-4c43-9b66-bf5d92f8641d/}\n\
    \n**audit\\_warning**: Processed alignments file {ENCFF913BSN|/files/ENCFF913BSN/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 18995697 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ UBTF-human and investigated as a transcription factor 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**:\
    \ 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 {ENCFF913BSN|/files/ENCFF913BSN/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with NRF value\
    \ of 0.58.\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 {ENCFF913BSN|/files/ENCFF913BSN/} processed by ChIP-seq\
    \ ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.57.\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 {ENCFF913BSN|/files/ENCFF913BSN/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ PBC2 value of 2.25.\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 {ENCFF337ZPN|/files/ENCFF337ZPN/},\
    \ {ENCFF030TJV|/files/ENCFF030TJV/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ have a rescue ratio of 2.54 and a self consistency ratio of 1.49. 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.\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 {ENCFF834LQR|/files/ENCFF834LQR/}, {ENCFF678AUZ|/files/ENCFF678AUZ/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 2.54 and\
    \ a self consistency ratio of 1.49. 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: ENCSR634ZGP
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens HeLa-S3
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002791/
    perturbed: false
    doi: 10.17989/ENCSR634ZGP
    date_created: '2015-03-27T17:30:15.652444+00:00'
    date_released: '2016-07-28'
    submitter_comment: As of June 2013, ENCODE has ceased work on the HeLa cell line.
      Though these data were released in 2016, the samples were prepared and sequenced
      in early 2013.
    target: UBTF