type: position_score
table:
  filename: ENCFF541VKE.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_ENCSR000EMJ
  column_index: 3
  type: float
  desc: 'DNase-seq ENCSR000EMJ [biosample_summary="Homo sapiens B cell female adult (43 years)"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'DNase-seq ENCSR000EMJ [biosample_summary="Homo sapiens B cell female adult (43 years)"]'
  description: '**status**: released


    **biological\_replicates**: Rep 1


    **summary**: female adult (43 years)


    **output\_type**: peaks


    **audit\_internal\_action**: Archived analysis {ENCAN556ZAU|/analyses/ENCAN556ZAU/}
    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 {ENCFF801IWM|/files/ENCFF801IWM/}, {ENCFF305QCJ|/files/ENCFF305QCJ/}
    processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/})
    for GRCh38 assembly  have a Pearson correlation of 0.89. 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 {ENCFF210XND|/files/ENCFF210XND/} processed
    by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} )
    for GRCh38 assembly has 33733574 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/})'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000EMJ
    status: released
    assay_term_name: DNase-seq
    simple_biosample_summary: female adult (43 years)
    biosample_summary: Homo sapiens B cell female adult (43 years)
    replication_type: isogenic
    biosample_ontology: /biosample-types/primary_cell_CL_0000236/
    perturbed: false
    doi: 10.17989/ENCSR000EMJ
    date_created: '2014-01-16T21:43:38.236873+00:00'
    date_released: '2011-10-19'
    submitter_comment: ''
