type: position_score
table:
  filename: ENCFF777DVJ.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_ENCSR075FNZ
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR075FNZ [biosample_summary="Homo sapiens GM12878" and target="ZNF622"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR075FNZ [biosample_summary="Homo sapiens GM12878" and target="ZNF622"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 3\n\
    \n**summary**: \n\n**output\\_type**: optimal IDR thresholded peaks\n\n**audit\\\
    _internal\\_action**: File {ENCFF777DVJ|/files/ENCFF777DVJ/} with status 'released'\
    \ is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'.\n\
    \n**audit\\_internal\\_action**: Archived analysis {ENCAN089BKF|/analyses/ENCAN089BKF/}\
    \ has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\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 {ENCFF993SEE|/files/ENCFF993SEE/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC1 value of 0.89.\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 {ENCFF993SEE|/files/ENCFF993SEE/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ PBC2 value of 8.74.\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 {ENCFF717ZWZ|/files/ENCFF717ZWZ/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 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 {ENCFF717ZWZ|/files/ENCFF717ZWZ/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC2 value of 7.44.\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 {ENCFF777DVJ|/files/ENCFF777DVJ/}, {ENCFF778TKQ|/files/ENCFF778TKQ/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.47 and\
    \ a self consistency ratio of 2.09. 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 {ENCFF368DYQ|/files/ENCFF368DYQ/},\
    \ {ENCFF191OAE|/files/ENCFF191OAE/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ have a rescue ratio of 1.47 and a self consistency ratio of 2.09. 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: ENCSR075FNZ
    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/ENCSR075FNZ
    date_created: '2016-05-13T20:18:06.615292+00:00'
    date_released: '2017-11-13'
    submitter_comment: ''
    target: ZNF622