type: position_score
table:
  filename: ENCFF917ZPO.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_ENCSR000BSE
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000BSE [biosample_summary="Homo sapiens HCT116" and target="CTCF"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000BSE [biosample_summary="Homo sapiens HCT116" and target="CTCF"]'
  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 {ENCAN626UKZ|/analyses/ENCAN626UKZ/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF296CPJ|/files/ENCFF296CPJ/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline has 6906852 usable fragments. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ CTCF-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**:\
    \ Processed alignments file {ENCFF555MNQ|/files/ENCFF555MNQ/} processed by ChIP-seq\
    \ ENCODE3 hg19 pipeline has 11875870 usable fragments. The minimum ENCODE standard\
    \ for each replicate in a ChIP-seq experiment targeting CTCF-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**: 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 {ENCFF296CPJ|/files/ENCFF296CPJ/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\
    \ PBC1 value of 0.88.\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 {ENCFF296CPJ|/files/ENCFF296CPJ/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ was generated from a library with PBC2 value of 8.09.\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 {ENCFF555MNQ|/files/ENCFF555MNQ/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with NRF value\
    \ of 0.77.\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 {ENCFF555MNQ|/files/ENCFF555MNQ/} processed by ChIP-seq\
    \ ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.80.\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 {ENCFF555MNQ|/files/ENCFF555MNQ/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\
    \ PBC2 value of 5.04.\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 {ENCFF917ZPO|/files/ENCFF917ZPO/},\
    \ {ENCFF025JZZ|/files/ENCFF025JZZ/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ have a rescue ratio of 1.19 and a self consistency ratio of 2.30. 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 {ENCFF272GUU|/files/ENCFF272GUU/}, {ENCFF239EKP|/files/ENCFF239EKP/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.19 and\
    \ a self consistency ratio of 2.30. 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: ENCSR000BSE
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens HCT116
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002824/
    perturbed: false
    doi: 10.17989/ENCSR000BSE
    date_created: '2013-12-19T20:51:49.249532+00:00'
    date_released: '2012-09-10'
    submitter_comment: ''
    target: CTCF