type: position_score
table:
  filename: ENCFF903KEI.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_ENCSR212YKD
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR212YKD [TISSUE: Homo sapiens GM12878, TARGET: SKIL]'
  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 {ENCAN803MTB|/analyses/ENCAN803MTB/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_internal\\_action**: File {ENCFF903KEI|/files/ENCFF903KEI/} with status\
    \ 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status\
    \ 'archived'.\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 {ENCFF065CIX|/files/ENCFF065CIX/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with NRF value of 0.48.\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\
    \ {ENCFF065CIX|/files/ENCFF065CIX/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ was generated from a library with PBC1 value of 0.47.\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 {ENCFF807RLO|/files/ENCFF807RLO/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with NRF value\
    \ of 0.45.\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 {ENCFF807RLO|/files/ENCFF807RLO/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value\
    \ of 0.46.\n\n**audit\\_warning**: Processed alignments file {ENCFF807RLO|/files/ENCFF807RLO/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 19322254 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ SKIL-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 {ENCFF065CIX|/files/ENCFF065CIX/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ PBC2 value of 1.84.\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 {ENCFF807RLO|/files/ENCFF807RLO/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC2 value of 1.88."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR212YKD
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens GM12878
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002784/
    perturbed: false
    doi: 10.17989/ENCSR212YKD
    date_created: '2015-09-29T21:34:01.292685+00:00'
    date_released: '2017-07-24'
    submitter_comment: Please note that the 'mixed platform' warning comes from the
      archived fastqs that were sequenced on the HiSeq2000 platform that if used,
      should be paired with the matching HiSeq2000 control ENCSR398JTO. The pipeline
      was run on the fastqs and controls sequenced on the HiSeq4000 platform for consistency.
    target: SKIL