type: position_score
table:
  filename: ENCFF632UNR.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_ENCSR000EPU
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'DNase-seq ENCSR000EPU [TISSUE: Homo sapiens epithelial cell of prostate]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 2\n\n**summary**:\
    \ \n\n**output\\_type**: peaks\n\n**audit\\_internal\\_action**: Archived analysis\
    \ {ENCAN574TXJ|/analyses/ENCAN574TXJ/} has in progress subobject quality standard\
    \ {encode3-dnase|/quality-standards/encode3-dnase/}\n\n**audit\\_warning**: Alignment\
    \ file {ENCFF222FBW|/files/ENCFF222FBW/} processed by DNase-seq ENCODE3 GRCh38\
    \ pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 35026810\
    \ 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 {ENCFF026UXE|/files/ENCFF026UXE/} processed\
    \ by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/}\
    \ ) for GRCh38 assembly has 35632996 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 {ENCFF879BNX|/files/ENCFF879BNX/} processed\
    \ by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/}\
    \ ) for GRCh38 assembly has 34705945 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 {ENCFF983FBQ|/files/ENCFF983FBQ/} processed\
    \ by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/}\
    \ ) for GRCh38 assembly has 35293367 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**: 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 {ENCFF879BNX|/files/ENCFF879BNX/} processed by DNase-seq ENCODE3\
    \ GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly\
    \  have a SPOT1 score of 0.33. 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\\\
    _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 {ENCFF983FBQ|/files/ENCFF983FBQ/} processed by DNase-seq ENCODE3 GRCh38\
    \ pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly  have a\
    \ SPOT1 score of 0.32. 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: ENCSR000EPU
    status: released
    assay_term_name: DNase-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens epithelial cell of prostate
    replication_type: isogenic
    biosample_ontology: /biosample-types/primary_cell_CL_0002231/
    perturbed: false
    doi: 10.17989/ENCSR000EPU
    date_created: '2013-12-12T07:09:52.520470+00:00'
    date_released: '2011-10-19'
    submitter_comment: ''
