type: position_score
table:
  filename: ENCFF319ZYX.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_ENCSR000EWD
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000EWD [biosample_summary="Homo sapiens K562" and target="SETDB1"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000EWD [biosample_summary="Homo sapiens K562" and target="SETDB1"]'
  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 {ENCAN448GDT|/analyses/ENCAN448GDT/} has in progress\
    \ subobject document {ec98bf22-6fe1-495c-a788-70e58a1fb8f3|/documents/ec98bf22-6fe1-495c-a788-70e58a1fb8f3/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN448GDT|/analyses/ENCAN448GDT/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF653VRH|/files/ENCFF653VRH/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 9748868 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ SETDB1-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\\\
    _not\\_compliant**: Replicate concordance in ChIP-seq experiments is measured\
    \ by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed\
    \ IDR thresholded peaks files {ENCFF319ZYX|/files/ENCFF319ZYX/} processed by ChIP-seq\
    \ ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 2.04 and a self consistency\
    \ ratio of 8.95. 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**: Processed alignments file\
    \ {ENCFF927KUH|/files/ENCFF927KUH/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38\
    \ pipeline has 10254303 usable fragments. The minimum ENCODE standard for each\
    \ replicate in a ChIP-seq experiment targeting SETDB1-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 {ENCFF927KUH|/files/ENCFF927KUH/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC1 value of 0.84.\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 {ENCFF927KUH|/files/ENCFF927KUH/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 6.00."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000EWD
    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/ENCSR000EWD
    date_created: '2014-02-12T23:01:28.332467+00:00'
    date_released: '2012-05-14'
    submitter_comment: The cross correlation for this ChIP-seq experiment was too
      poor for peaks to be called.
    target: SETDB1