type: position_score
table:
  filename: ENCFF134JLR.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_ENCSR720HUL
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR720HUL [TISSUE: Homo sapiens K562, TARGET: E2F1]'
  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**: File {ENCFF134JLR|/files/ENCFF134JLR/} with status 'released'\
    \ is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'.\n\
    \n**audit\\_internal\\_action**: Archived analysis {ENCAN848OMH|/analyses/ENCAN848OMH/}\
    \ has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\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 {ENCFF508JKO|/files/ENCFF508JKO/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ NRF value of 0.41.\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 {ENCFF508JKO|/files/ENCFF508JKO/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value\
    \ of 0.45.\n\n**audit\\_warning**: Processed alignments file {ENCFF508JKO|/files/ENCFF508JKO/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 13374276 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ E2F1-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 {ENCFF260TPL|/files/ENCFF260TPL/} processed by ChIP-seq\
    \ ENCODE3 GRCh38 pipeline has 15125688 usable fragments. The minimum ENCODE standard\
    \ for each replicate in a ChIP-seq experiment targeting E2F1-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**: 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 {ENCFF508JKO|/files/ENCFF508JKO/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC2 value of 1.93.\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 {ENCFF260TPL|/files/ENCFF260TPL/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ NRF value of 0.57.\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 {ENCFF260TPL|/files/ENCFF260TPL/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value\
    \ of 0.58.\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 {ENCFF260TPL|/files/ENCFF260TPL/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC2 value of 2.42."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR720HUL
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens K562
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002067/
    perturbed: false
    doi: 10.17989/ENCSR720HUL
    date_created: '2016-04-27T19:03:12.727694+00:00'
    date_released: '2018-01-26'
    submitter_comment: 'We note that this ChIP-seq experiment was performed using
      an antibody for which we have provided a compliant primary characterization
      but no secondary characterization.  A secondary characterization using IP-MS
      was attempted, but the experiment failed.  There is no remaining antibody from
      this lot number and therefore additional secondary characterizations cannot
      be attempted. However, because the replicate ChIP-seq datasets passed the ENCODE
      IDR ChIP-seq data quality standards, we are releasing the data to the public.
      This experiment was used in the ENCODE-DREAM Transcription Factor Binding Site
      Prediction Challenge (https://www.synapse.org/#!Synapse:syn6131484/wiki/400026).
      IMPORTANT: This experiment and ENCSR531KJT were both part of the DREAM challenge
      but have since been merged as they were the same libraries, just sequenced on
      two different platforms. The original analysis files have been archived. This
      experiment was re-processed using a control sequenced on HiSeq4000 rather than
      on HiSeq2000 as it was originally done so the platforms now match.'
    target: E2F1