type: position_score
table:
  filename: ENCFF581YKY.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_ENCSR986CDX
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR986CDX [biosample_summary="Homo sapiens K562" and target="NEUROD1"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR986CDX [biosample_summary="Homo sapiens K562" and target="NEUROD1"]'
  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 {ENCAN671TLH|/analyses/ENCAN671TLH/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_warning**: Processed alignments file {ENCFF325ZZV|/files/ENCFF325ZZV/}\
    \ processed by ChIP-seq ENCODE3 hg19 pipeline has 18767322 usable fragments. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ NEUROD1-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 {ENCFF637BQA|/files/ENCFF637BQA/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline has 10716907 usable fragments. The minimum\
    \ ENCODE standard for each replicate in a ChIP-seq experiment targeting NEUROD1-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**:\
    \ Replicate concordance in ChIP-seq experiments is measured by calculating IDR\
    \ values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks\
    \ files {ENCFF852XSD|/files/ENCFF852XSD/}, {ENCFF581YKY|/files/ENCFF581YKY/} processed\
    \ by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.37 and a self consistency\
    \ ratio of 4.35. 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 {ENCFF823QCH|/files/ENCFF823QCH/},\
    \ {ENCFF872LIG|/files/ENCFF872LIG/} processed by ChIP-seq ENCODE3 hg19 pipeline\
    \ have a rescue ratio of 1.37 and a self consistency ratio of 4.35. 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: ENCSR986CDX
    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/ENCSR986CDX
    date_created: '2014-07-02T22:44:29.837536+00:00'
    date_released: '2014-07-07'
    submitter_comment: We note that this ChIP-seq experiment was performed using an
      antibody for which we have provided a compliant primary characterization but
      no secondary characterization.  A secondary characterization using IP-MS was
      attempted, but the experiment failed.  There is no remaining antibody from this
      lot number and therefore additional secondary characterizations cannot be attempted.
      However, because the replicate ChIP-seq datasets passed the ENCODE IDR ChIP-seq
      data quality standards, we are releasing the data to the public.
    target: NEUROD1
