type: position_score
table:
  filename: ENCFF556SMM.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_ENCSR028UIU
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR028UIU [biosample_summary="Homo sapiens K562" and target="ATF3"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR028UIU [biosample_summary="Homo sapiens K562" and target="ATF3"]'
  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 {ENCAN514OAL|/analyses/ENCAN514OAL/} has in progress\
    \ subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN514OAL|/analyses/ENCAN514OAL/}\
    \ has in progress subobject document {a5cc2512-c87d-46db-87de-a45a8cf176ba|/documents/a5cc2512-c87d-46db-87de-a45a8cf176ba/}\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 {ENCFF593CDF|/files/ENCFF593CDF/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with PBC1 value of 0.81.\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 {ENCFF593CDF|/files/ENCFF593CDF/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 5.12.\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 {ENCFF316FLH|/files/ENCFF316FLH/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with NRF value of 0.69.\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\
    \ {ENCFF316FLH|/files/ENCFF316FLH/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38\
    \ pipeline was generated from a library with PBC1 value of 0.68.\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 {ENCFF316FLH|/files/ENCFF316FLH/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 3.08."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR028UIU
    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/ENCSR028UIU
    date_created: '2016-04-27T18:29:59.800825+00:00'
    date_released: '2016-07-08'
    submitter_comment: 'This experiment is being used in the ENCODE-DREAM Transcription
      Factor Binding Site Prediction Challenge (https://www.synapse.org/#!Synapse:syn6131484/wiki/400026).
      The files will be unavailable until after the challenge completes on 09-30-16.
      UPDATE: There will be a second round to the challenge that is expected to end
      on 01-11-2017. IMPORTANT: When this experiment was released for DREAM, it was
      matched with possible_control = ENCSR173USI, which was an input control sequenced
      on HiSeq2000. We have since associated an input control with matching sequencing
      platform (HiSeq4000) instead.'
    target: ATF3
