type: position_score
table:
  filename: ENCFF514WJW.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_ENCSR711SNW
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR711SNW [biosample_summary="Homo sapiens K562" and target="NCOA1"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR711SNW [biosample_summary="Homo sapiens K562" and target="NCOA1"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: IDR thresholded peaks\n\n**audit\\_internal\\\
    _action**: Released analysis {ENCAN625OKZ|/analyses/ENCAN625OKZ/} has in progress\
    \ subobject document {72a54484-4df0-462f-962a-193460ca8a0a|/documents/72a54484-4df0-462f-962a-193460ca8a0a/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN625OKZ|/analyses/ENCAN625OKZ/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_warning**: Processed alignments file {ENCFF241PTS|/files/ENCFF241PTS/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 13492741 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ NCOA1-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 {ENCFF426PPM|/files/ENCFF426PPM/} processed\
    \ by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 18429480 usable fragments. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ NCOA1-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 {ENCFF241PTS|/files/ENCFF241PTS/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.72.\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 {ENCFF241PTS|/files/ENCFF241PTS/} processed\
    \ by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with\
    \ PBC1 value of 0.72.\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 {ENCFF241PTS|/files/ENCFF241PTS/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 3.56.\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 {ENCFF426PPM|/files/ENCFF426PPM/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.78.\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 {ENCFF426PPM|/files/ENCFF426PPM/} processed\
    \ by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with\
    \ PBC1 value of 0.77.\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 {ENCFF426PPM|/files/ENCFF426PPM/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 4.33."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR711SNW
    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/ENCSR711SNW
    date_created: '2015-06-30T21:32:24.244379+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.
    target: NCOA1