type: position_score
table:
  filename: ENCFF220TWO.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_ENCSR000EKD
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'DNase-seq ENCSR000EKD [TISSUE: Homo sapiens HuH-7]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1\n\n**summary**:\
    \ \n\n**output\\_type**: peaks\n\n**audit\\_error**: Alignment file {ENCFF172VLC|/files/ENCFF172VLC/}\
    \ processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/}\
    \ ) for GRCh38 assembly has 249407 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/})\n\
    \n**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 {ENCFF172VLC|/files/ENCFF172VLC/} processed by DNase-seq ENCODE3\
    \ GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly\
    \  have a SPOT1 score of 0.22. 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/})\n\n**audit\\\
    _internal\\_action**: Archived analysis {ENCAN803FVU|/analyses/ENCAN803FVU/} has\
    \ in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/}"
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000EKD
    status: released
    assay_term_name: DNase-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens HuH-7
    replication_type: unreplicated
    biosample_ontology: /biosample-types/cell_line_EFO_0005384/
    perturbed: false
    doi: 10.17989/ENCSR000EKD
    date_created: '2013-12-12T07:07:39.837618+00:00'
    date_released: '2011-04-19'
    submitter_comment: ''