type: position_score
table:
  filename: ENCFF298UPI.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_ENCSR459FTB
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR459FTB [biosample_summary="Homo sapiens GM12878" and target="UBTF"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR459FTB [biosample_summary="Homo sapiens GM12878" and target="UBTF"]'
  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 {ENCAN214FDK|/analyses/ENCAN214FDK/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_warning**: Processed alignments file {ENCFF370YOR|/files/ENCFF370YOR/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline has 19400374 usable fragments. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ UBTF-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 {ENCFF688XDE|/files/ENCFF688XDE/} processed by ChIP-seq\
    \ ENCODE3 hg19 pipeline has 13021124 usable fragments. The minimum ENCODE standard\
    \ for each replicate in a ChIP-seq experiment targeting UBTF-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 {ENCFF688XDE|/files/ENCFF688XDE/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\
    \ PBC1 value of 0.87.\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 {ENCFF688XDE|/files/ENCFF688XDE/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ was generated from a library with PBC2 value of 7.71.\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 {ENCFF754GFB|/files/ENCFF754GFB/}, {ENCFF802EUE|/files/ENCFF802EUE/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.46 and a self consistency\
    \ ratio of 2.54. 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 {ENCFF930SKY|/files/ENCFF930SKY/},\
    \ {ENCFF846HFA|/files/ENCFF846HFA/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ have a rescue ratio of 1.57 and a self consistency ratio of 2.66. 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 {ENCFF499CTR|/files/ENCFF499CTR/}, {ENCFF745TNJ|/files/ENCFF745TNJ/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.46 and\
    \ a self consistency ratio of 2.54. 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 {ENCFF298UPI|/files/ENCFF298UPI/},\
    \ {ENCFF791WCX|/files/ENCFF791WCX/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ have a rescue ratio of 1.57 and a self consistency ratio of 2.66. 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: ENCSR459FTB
    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/ENCSR459FTB
    date_created: '2014-07-02T22:44:15.842745+00:00'
    date_released: '2014-07-07'
    submitter_comment: ''
    target: UBTF
