type: position_score
table:
  filename: ENCFF229SJW.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_ENCSR000EPH
  column_index: 3
  type: float
  desc: 'DNase-seq ENCSR000EPH [biosample_summary="Homo sapiens MCF-7"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'DNase-seq ENCSR000EPH [biosample_summary="Homo sapiens MCF-7"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 2\n\n**summary**:\
    \ \n\n**output\\_type**: peaks\n\n**audit\\_internal\\_action**: Archived analysis\
    \ {ENCAN069OPA|/analyses/ENCAN069OPA/} has in progress subobject quality standard\
    \ {encode3-dnase|/quality-standards/encode3-dnase/}\n\n**audit\\_warning**: Alignment\
    \ file {ENCFF100MIL|/files/ENCFF100MIL/} processed by DNase-seq ENCODE3 GRCh38\
    \ pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 44796019\
    \ 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\\_warning**: Alignment file {ENCFF955DEC|/files/ENCFF955DEC/} processed\
    \ by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/}\
    \ ) for GRCh38 assembly has 44577938 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: ENCSR000EPH
    status: released
    assay_term_name: DNase-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens MCF-7
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0001203/
    perturbed: false
    doi: 10.17989/ENCSR000EPH
    date_created: '2013-12-12T07:09:37.474210+00:00'
    date_released: '2012-06-12'
    submitter_comment: ''