type: position_score
table:
  filename: ENCFF624NUZ.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_ENCSR724GSW
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR724GSW [biosample_summary="Homo sapiens K562" and target="SAFB2"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR724GSW [biosample_summary="Homo sapiens K562" and target="SAFB2"]'
  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**: Released analysis {ENCAN449YQK|/analyses/ENCAN449YQK/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\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 {ENCFF836GWP|/files/ENCFF836GWP/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ was generated from a library with PBC1 value of 0.38.\n\n**audit\\_not\\_compliant**:\
    \ 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 {ENCFF836GWP|/files/ENCFF836GWP/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\
    \ PBC2 value of 0.70.\n\n**audit\\_warning**: Processed alignments file {ENCFF431ABA|/files/ENCFF431ABA/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline has 12659312 usable fragments. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ SAFB2-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 {ENCFF836GWP|/files/ENCFF836GWP/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline has 14727782 usable fragments. The minimum\
    \ ENCODE standard for each replicate in a ChIP-seq experiment targeting SAFB2-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 {ENCFF836GWP|/files/ENCFF836GWP/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with NRF value\
    \ of 0.57.\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 {ENCFF550DYZ|/files/ENCFF550DYZ/}, {ENCFF624NUZ|/files/ENCFF624NUZ/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.29 and\
    \ a self consistency ratio of 2.97. 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.\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 {ENCFF520GWJ|/files/ENCFF520GWJ/},\
    \ {ENCFF265TAY|/files/ENCFF265TAY/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ have a rescue ratio of 1.29 and a self consistency ratio of 2.97. 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: ENCSR724GSW
    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/ENCSR724GSW
    date_created: '2014-11-27T18:22:17.447643+00:00'
    date_released: '2018-01-26'
    submitter_comment: ''
    target: SAFB2
