type: position_score
table:
  filename: ENCFF883EGI.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_ENCSR000BQF
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000BQF [biosample_summary="Homo sapiens SK-N-SH" and target="TAF1"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000BQF [biosample_summary="Homo sapiens SK-N-SH" and target="TAF1"]'
  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 {ENCAN631RSP|/analyses/ENCAN631RSP/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_warning**: Processed alignments file {ENCFF916OWO|/files/ENCFF916OWO/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline has 18343639 usable fragments. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ TAF1-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 {ENCFF185JZF|/files/ENCFF185JZF/} processed by ChIP-seq\
    \ ENCODE3 hg19 pipeline has 16249647 usable fragments. The minimum ENCODE standard\
    \ for each replicate in a ChIP-seq experiment targeting TAF1-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 {ENCFF916OWO|/files/ENCFF916OWO/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ was generated from a library with NRF value of 0.73.\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\
    \ {ENCFF916OWO|/files/ENCFF916OWO/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ was generated from a library with PBC1 value of 0.71.\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 {ENCFF916OWO|/files/ENCFF916OWO/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\
    \ PBC2 value of 3.32.\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 {ENCFF185JZF|/files/ENCFF185JZF/} processed\
    \ by ChIP-seq ENCODE3 hg19 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 {ENCFF185JZF|/files/ENCFF185JZF/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ was generated from a library with PBC2 value of 5.22.\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 {ENCFF950OCE|/files/ENCFF950OCE/}, {ENCFF883EGI|/files/ENCFF883EGI/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.34 and a self consistency\
    \ ratio of 2.33. 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 {ENCFF078DBD|/files/ENCFF078DBD/},\
    \ {ENCFF591NTQ|/files/ENCFF591NTQ/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ have a rescue ratio of 1.34 and a self consistency ratio of 2.33. 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: ENCSR000BQF
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens SK-N-SH
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0003072/
    perturbed: false
    doi: 10.17989/ENCSR000BQF
    date_created: '2013-09-13T16:52:43.471097-08:00'
    date_released: '2012-02-29'
    submitter_comment: ''
    target: TAF1