type: position_score
table:
  filename: ENCFF129OYC.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: ATAC-seq_ENCSR729FNL
  column_index: 3
  type: float
  desc: 'ATAC-seq ENCSR729FNL [biosample_summary="Homo sapiens posterior cingulate cortex tissue male adult (20 years)"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR729FNL [biosample_summary="Homo sapiens posterior cingulate cortex tissue male adult (20 years)"]'
  description: '**status**: released


    **biological\_replicates**: Rep 1


    **summary**: male adult (20 years)


    **output\_type**: pseudoreplicated peaks


    **audit\_internal\_action**: Released analysis {ENCAN343RLI|/analyses/ENCAN343RLI/}
    has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}


    **audit\_not\_compliant**: According to ENCODE4 standards, overlap peaks files
    in ATAC-seq assays processed by the uniform processing pipeline should have FRiP
    (fraction of reads in called peak regions) scores > 0.3. FRiP scores 0.2-0.3 are
    acceptable, and < 0.2 are not compliant. {ENCFF129OYC|/files/ENCFF129OYC/} processed
    by ATAC-seq ENCODE4 v1.9.2 GRCh38 pipeline  has a FRiP score of 0.04.


    **audit\_not\_compliant**: According to ENCODE4 standards, ATAC-seq assays processed
    by the uniform processing pipeline should have either >150k reproducible peaks
    in an overlap peaks file, or >70k in an IDR thresholded peaks file. 100-150k or
    50-70k peaks respectively is acceptable, and <100k or <50k respectively is not
    compliant. File(s) {ENCFF129OYC|/files/ENCFF129OYC/} (overlap peaks) and {ENCFF221FSW|/files/ENCFF221FSW/}
    (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.2 GRCh38 pipeline have
    39396 and 11331 peaks.


    **audit\_warning**: Transcription Start Site (TSS) enrichment values for alignments
    to the human genome GRCh38 are concerning when < 5, acceptable between 5 and 7,
    and ideal when > 7. ENCODE processed file {ENCFF876ELG|/files/ENCFF876ELG/} processed
    by ATAC-seq ENCODE4 v1.9.2 GRCh38 pipeline has a TSS enrichment value of 5.992365727913902.


    **audit\_warning**: NRF (Non Redundant Fraction) is equal to the result of the
    division of the number of reads after duplicates removal by the total number of
    reads. An NRF value < 0.7 is poor complexity, between 0.7 and 0.9 is moderate
    complexity, and >= 0.9 high complexity. NRF value > 0.9 is recommended, but >
    0.7 is acceptable. ENCODE processed file {ENCFF876ELG|/files/ENCFF876ELG/} processed
    by ATAC-seq ENCODE4 v1.9.2 GRCh38 pipeline was generated from a library with NRF
    value of 0.857676.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR729FNL
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: male adult (20 years)
    biosample_summary: Homo sapiens posterior cingulate cortex tissue male adult (20
      years)
    replication_type: unreplicated
    biosample_ontology: /biosample-types/tissue_UBERON_0022353/
    perturbed: false
    doi: 10.17989/ENCSR729FNL
    date_created: '2015-11-26T00:01:33.328366+00:00'
    date_released: '2017-10-09'
    submitter_comment: ''
