type: position_score
table:
  filename: ENCFF492ZRZ.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_ENCSR000BGQ
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000BGQ [biosample_summary="Homo sapiens GM12878" and target="SPI1"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000BGQ [biosample_summary="Homo sapiens GM12878" and target="SPI1"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 2, Rep 3\n\
    \n**summary**: \n\n**output\\_type**: IDR thresholded peaks\n\n**audit\\_internal\\\
    _action**: Released analysis {ENCAN852XWQ|/analyses/ENCAN852XWQ/} has in progress\
    \ subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF086XFU|/files/ENCFF086XFU/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 9421990 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ SPI1-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 {ENCFF436HQW|/files/ENCFF436HQW/} processed by ChIP-seq\
    \ ENCODE4 v1.6.1 GRCh38 pipeline has 19092128 usable fragments. The minimum ENCODE\
    \ standard for each replicate in a ChIP-seq experiment targeting SPI1-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**: 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 {ENCFF436HQW|/files/ENCFF436HQW/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC1 value of 0.86.\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 {ENCFF436HQW|/files/ENCFF436HQW/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 7.85.\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 {ENCFF086XFU|/files/ENCFF086XFU/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.65.\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 {ENCFF086XFU|/files/ENCFF086XFU/} processed\
    \ by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with\
    \ PBC1 value of 0.65.\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 {ENCFF086XFU|/files/ENCFF086XFU/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 2.82.\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 {ENCFF492ZRZ|/files/ENCFF492ZRZ/} processed by ChIP-seq ENCODE4\
    \ v1.6.1 GRCh38 pipeline have a rescue ratio of 1.43 and a self consistency ratio\
    \ of 2.60. 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: ENCSR000BGQ
    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/ENCSR000BGQ
    date_created: '2013-09-13T16:01:54.695587-08:00'
    date_released: '2011-07-18'
    submitter_comment: ''
    target: SPI1