type: position_score
table:
  filename: ENCFF463DWW.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_ENCSR000BUQ
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000BUQ [biosample_summary="Homo sapiens SK-N-SH" and target="TEAD4"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000BUQ [biosample_summary="Homo sapiens SK-N-SH" and target="TEAD4"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: IDR thresholded peaks\n\n**audit\\_internal\\\
    _action**: Released analysis {ENCAN393ETY|/analyses/ENCAN393ETY/} has in progress\
    \ subobject document {1b3ae27e-e0d3-4cff-9881-1776da6f36e1|/documents/1b3ae27e-e0d3-4cff-9881-1776da6f36e1/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN393ETY|/analyses/ENCAN393ETY/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF031WOZ|/files/ENCFF031WOZ/}\
    \ processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline has 8540741 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ TEAD4-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\
    \ {ENCFF031WOZ|/files/ENCFF031WOZ/} processed by ChIP-seq ENCODE4 v1.4.0 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 {ENCFF031WOZ|/files/ENCFF031WOZ/}\
    \ processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 7.81.\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 {ENCFF463DWW|/files/ENCFF463DWW/}\
    \ processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of\
    \ 1.14 and a self consistency ratio of 2.31. 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 {ENCFF754TJT|/files/ENCFF754TJT/} processed by ChIP-seq ENCODE4 v1.4.0\
    \ GRCh38 pipeline have a rescue ratio of 1.14 and a self consistency ratio of\
    \ 2.31. 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: ENCSR000BUQ
    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/ENCSR000BUQ
    date_created: '2013-09-13T16:00:47.625043-08:00'
    date_released: '2012-09-10'
    submitter_comment: ''
    target: TEAD4