type: position_score
table:
  filename: ENCFF938CRS.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_ENCSR125DKL
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR125DKL [TISSUE: Homo sapiens SU-DHL-6, TARGET: CTCF]'
  description: "**status**: archived\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 {ENCAN550MIQ|/analyses/ENCAN550MIQ/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF749AWO|/files/ENCFF749AWO/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 9083118 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\\_not\\\
    _compliant**: 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 {ENCFF749AWO|/files/ENCFF749AWO/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ NRF value of 0.38.\n\n**audit\\_not\\_compliant**: 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 {ENCFF749AWO|/files/ENCFF749AWO/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value\
    \ of 0.36.\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 {ENCFF749AWO|/files/ENCFF749AWO/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC2 value of 1.66.\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 {ENCFF310IBX|/files/ENCFF310IBX/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ NRF value of 0.74.\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 {ENCFF310IBX|/files/ENCFF310IBX/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value\
    \ of 0.73.\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 {ENCFF310IBX|/files/ENCFF310IBX/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC2 value of 3.71.\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 {ENCFF938CRS|/files/ENCFF938CRS/} processed by ChIP-seq ENCODE3\
    \ GRCh38 pipeline have a rescue ratio of 1.20 and a self consistency ratio of\
    \ 2.07. 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 {ENCFF602PMH|/files/ENCFF602PMH/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.20 and a self consistency\
    \ ratio of 2.07. 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: ENCSR125DKL
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens SU-DHL-6
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002357/
    perturbed: false
    doi: 10.17989/ENCSR125DKL
    date_created: '2014-02-20T05:43:10.694519+00:00'
    date_released: '2017-11-29'
    submitter_comment: As of March 1st, 2018, this experiment is being re-run on a
      new ENCODE ChIP-seq pipeline.
    target: CTCF