type: position_score
table:
  filename: ENCFF186QHO.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_ENCSR682PKY
  column_index: 3
  type: float
  desc: 'DNase-seq ENCSR682PKY [biosample_summary="Homo sapiens thymus tissue female embryo"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'DNase-seq ENCSR682PKY [biosample_summary="Homo sapiens thymus tissue female embryo"]'
  description: '**status**: released


    **biological\_replicates**: Rep 1


    **summary**: female embryo


    **output\_type**: peaks


    **audit\_internal\_action**: Archived analysis {ENCAN519MPX|/analyses/ENCAN519MPX/}
    has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/}


    **audit\_warning**: Alignment file {ENCFF810FRM|/files/ENCFF810FRM/} processed
    by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} )
    for GRCh38 assembly has 32705402 mapped reads. According to ENCODE standards,
    conventional DNase-seq profile requires a minimum of 20 million uniquely mapped
    reads to generate a reliable SPOT (Signal Portion of Tags) score. The recommended
    value is > 50 million. For deep, foot-printing depth DNase-seq 150-200 million
    uniquely mapped reads are recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq/})


    **audit\_warning**: Alignment file {ENCFF139RJL|/files/ENCFF139RJL/} processed
    by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} )
    for GRCh38 assembly has 32461431 mapped reads. According to ENCODE standards,
    conventional DNase-seq profile requires a minimum of 20 million uniquely mapped
    reads to generate a reliable SPOT (Signal Portion of Tags) score. The recommended
    value is > 50 million. For deep, foot-printing depth DNase-seq 150-200 million
    uniquely mapped reads are 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 {ENCFF139RJL|/files/ENCFF139RJL/} processed by DNase-seq ENCODE3
    GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly  have
    a SPOT1 score of 0.40. 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: ENCSR682PKY
    status: released
    assay_term_name: DNase-seq
    simple_biosample_summary: female embryo
    biosample_summary: Homo sapiens thymus tissue female embryo
    replication_type: unreplicated
    biosample_ontology: /biosample-types/tissue_UBERON_0002370/
    perturbed: false
    doi: 10.17989/ENCSR682PKY
    date_created: '2015-09-16T21:43:02.729663+00:00'
    date_released: '2013-07-31'
    submitter_comment: ''