type: position_score
table:
  filename: ENCFF551YAW.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: DNase-seq_ENCSR532CRI
  column_index: 3
  type: float
  desc: 'DNase-seq ENCSR532CRI [biosample_summary="Homo sapiens limb tissue embryo (58 days) and embryo (59 days)"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'DNase-seq ENCSR532CRI [biosample_summary="Homo sapiens limb tissue embryo (58 days) and embryo (59 days)"]'
  description: '**status**: released


    **biological\_replicates**: Rep 2


    **summary**: embryo (59 days) embryo (58 days)


    **output\_type**: peaks


    **audit\_error**: Signal Portion of Tags (SPOT) is a measure of enrichment, analogous
    to the commonly used fraction of reads in peaks metric. ENCODE processed alignment
    files {ENCFF371ZLX|/files/ENCFF371ZLX/} processed by DNase-seq ENCODE3 GRCh38
    pipeline ({ENCPL202DNS|/pipelines/ENCPL202DNS/}) for GRCh38 assembly  have a SPOT1
    score of 0.25. According to ENCODE standards, SPOT1 score of 0.4 or higher is
    considered a product of high quality data. Any sample with a SPOT1 score <0.3
    should be targeted for replacement with a higher quality sample, and a SPOT1 score
    of 0.25 is considered minimally acceptable SPOT1 score of 0.25 is considered minimally
    acceptable for rare and hard to find primary tissues. (See {ENCODE DNase-seq data
    standards|/data-standards/dnase-seq/})


    **audit\_internal\_action**: Archived analysis {ENCAN929UJL|/analyses/ENCAN929UJL/}
    has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/}


    **audit\_not\_compliant**: Replicate concordance in DNase-seq experiments is measured
    by calculating the Pearson correlation between signal quantification of the replicates.
    ENCODE processed signal files {ENCFF850IPE|/files/ENCFF850IPE/}, {ENCFF135BMZ|/files/ENCFF135BMZ/}
    processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL202DNS|/pipelines/ENCPL202DNS/})
    for GRCh38 assembly  have a Pearson correlation of 0.83. According to ENCODE standards,
    in an anisogenic assay a Pearson correlation value > 0.85 is recommended. (See
    {ENCODE DNase-seq data standards|/data-standards/dnase-seq/} )


    **audit\_warning**: Signal Portion of Tags (SPOT) is a measure of enrichment,
    analogous to the commonly used fraction of reads in peaks metric. ENCODE processed
    alignment files {ENCFF757WSE|/files/ENCFF757WSE/} processed by DNase-seq ENCODE3
    GRCh38 pipeline ({ENCPL202DNS|/pipelines/ENCPL202DNS/}) for GRCh38 assembly  have
    a SPOT1 score of 0.25. According to ENCODE standards, SPOT1 score of 0.4 or higher
    is considered a product of high quality data. Any sample with a SPOT1 score <0.3
    should be targeted for replacement with a higher quality sample, and a SPOT1 score
    of 0.25 is considered minimally acceptable SPOT1 score of 0.25 is considered minimally
    acceptable for rare and hard to find primary tissues. (See {ENCODE DNase-seq data
    standards|/data-standards/dnase-seq/})'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR532CRI
    status: released
    assay_term_name: DNase-seq
    simple_biosample_summary: embryo (58 days) embryo (59 days)
    biosample_summary: Homo sapiens limb tissue embryo (58 days) and embryo (59 days)
    replication_type: anisogenic
    biosample_ontology: /biosample-types/tissue_UBERON_0002101/
    perturbed: false
    doi: 10.17989/ENCSR532CRI
    date_created: '2015-12-15T05:47:46.379578+00:00'
    date_released: '2016-05-09'
    submitter_comment: ''
