type: position_score
table:
  filename: ENCFF759OLD.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_ENCSR000EMT
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'DNase-seq ENCSR000EMT [TISSUE: Homo sapiens GM12878]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 2\n\n**summary**:\
    \ \n\n**output\\_type**: peaks\n\n**audit\\_warning**: Alignment file {ENCFF020WZB|/files/ENCFF020WZB/}\
    \ processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/}\
    \ ) for GRCh38 assembly has 22289382 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-encode4/})\n\
    \n**audit\\_warning**: Alignment file {ENCFF729UYK|/files/ENCFF729UYK/} processed\
    \ by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/}\
    \ ) for GRCh38 assembly has 38560136 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-encode4/})\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 {ENCFF020WZB|/files/ENCFF020WZB/} processed by DNase-seq ENCODE4\
    \ v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38\
    \ assembly  have a SPOT1 score of 0.39. 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-encode4/})\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 {ENCFF729UYK|/files/ENCFF729UYK/} processed by DNase-seq ENCODE4\
    \ v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38\
    \ assembly  have a SPOT1 score of 0.36. 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-encode4/})"
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000EMT
    status: released
    assay_term_name: DNase-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens GM12878
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002784/
    perturbed: false
    doi: 10.17989/ENCSR000EMT
    date_created: '2013-09-13T15:58:20.192893-08:00'
    date_released: '2011-05-04'
    submitter_comment: 'Fastq file ENCFF001CWQ contains reads of mixed lengths. Read
      lengths followed by respective number of reads: (28, 12699243), (36, 162429412)'