type: position_score
table:
  filename: ENCFF216YDM.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_ENCSR000EZC
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000EZC [biosample_summary="Homo sapiens HeLa-S3" and target="SMARCA4"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000EZC [biosample_summary="Homo sapiens HeLa-S3" and target="SMARCA4"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2,\
    \ Rep 3\n\n**summary**: \n\n**output\\_type**: IDR thresholded peaks\n\n**audit\\\
    _internal\\_action**: Released analysis {ENCAN903WDS|/analyses/ENCAN903WDS/} has\
    \ in progress subobject document {ba7e5fb8-3463-4c8a-89e8-31cb074894ed|/documents/ba7e5fb8-3463-4c8a-89e8-31cb074894ed/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN903WDS|/analyses/ENCAN903WDS/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF557YXZ|/files/ENCFF557YXZ/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 5738638 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ SMARCA4-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**: Processed alignments file {ENCFF335CUS|/files/ENCFF335CUS/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 5779653 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ SMARCA4-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**: Processed alignments file {ENCFF970BHF|/files/ENCFF970BHF/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 5102105 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ SMARCA4-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 {ENCFF216YDM|/files/ENCFF216YDM/} processed by ChIP-seq\
    \ ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 4.45 and a self consistency\
    \ ratio of 4.60. 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: ENCSR000EZC
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens HeLa-S3
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002791/
    perturbed: false
    doi: 10.17989/ENCSR000EZC
    date_created: '2013-12-12T07:14:36.206673+00:00'
    date_released: '2011-10-29'
    submitter_comment: ''
    target: SMARCA4
