type: position_score
table:
  filename: ENCFF742OKP.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_ENCSR000EQE
  column_index: 3
  type: float
  desc: 'DNase-seq ENCSR000EQE [biosample_summary="Homo sapiens T-helper 1 cell male adult (33 years)"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'DNase-seq ENCSR000EQE [biosample_summary="Homo sapiens T-helper 1 cell male adult (33 years)"]'
  description: '**status**: released


    **biological\_replicates**: Rep 1


    **summary**: male adult (33 years)


    **output\_type**: peaks


    **audit\_internal\_action**: Archived analysis {ENCAN957AEM|/analyses/ENCAN957AEM/}
    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 {ENCFF795TGF|/files/ENCFF795TGF/}, {ENCFF730AXF|/files/ENCFF730AXF/}
    processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/})
    for GRCh38 assembly  have a Pearson correlation of 0.85. According to ENCODE standards,
    in an isogenic assay a Pearson correlation value > 0.9 is recommended. (See {ENCODE
    DNase-seq data standards|/data-standards/dnase-seq/} )


    **audit\_warning**: Alignment file {ENCFF329FPF|/files/ENCFF329FPF/} processed
    by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} )
    for GRCh38 assembly has 20520963 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 {ENCFF437UDA|/files/ENCFF437UDA/} processed
    by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} )
    for GRCh38 assembly has 20373691 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 {ENCFF765IRM|/files/ENCFF765IRM/} processed by DNase-seq ENCODE3
    GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) 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\_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 {ENCFF437UDA|/files/ENCFF437UDA/} processed by DNase-seq ENCODE3
    GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly  have
    a SPOT1 score of 0.34. 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: ENCSR000EQE
    status: released
    assay_term_name: DNase-seq
    simple_biosample_summary: male adult (33 years)
    biosample_summary: Homo sapiens T-helper 1 cell male adult (33 years)
    replication_type: isogenic
    biosample_ontology: /biosample-types/primary_cell_CL_0000545/
    perturbed: false
    doi: 10.17989/ENCSR000EQE
    date_created: '2013-12-12T07:10:04.409539+00:00'
    date_released: '2012-07-23'
    submitter_comment: ''
