type: position_score
table:
  filename: ENCFF030AIT.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_ENCSR999NKW
  column_index: 3
  type: float
  desc: 'ATAC-seq ENCSR999NKW [biosample_summary="Homo sapiens prostate gland tissue male adult (54 years)"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR999NKW [biosample_summary="Homo sapiens prostate gland tissue male adult (54 years)"]'
  description: '**status**: released


    **biological\_replicates**: Rep 1


    **summary**: male adult (54 years)


    **output\_type**: pseudoreplicated peaks


    **audit\_internal\_action**: Released analysis {ENCAN518UZV|/analyses/ENCAN518UZV/}
    has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}


    **audit\_internal\_action**: Released analysis {ENCAN518UZV|/analyses/ENCAN518UZV/}
    has in progress subobject document {7e497c52-6f63-4231-bc89-c15a5f751eb4|/documents/7e497c52-6f63-4231-bc89-c15a5f751eb4/}


    **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. {ENCFF030AIT|/files/ENCFF030AIT/} processed
    by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline  has a FRiP score of 0.06.


    **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) {ENCFF030AIT|/files/ENCFF030AIT/} (overlap peaks) and {ENCFF963ISM|/files/ENCFF963ISM/}
    (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have
    65658 and 20844 peaks.


    **audit\_warning**: Alignment file {ENCFF678CZL|/files/ENCFF678CZL/} processed
    by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 21947987 usable fragments. According
    to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline
    should have > 25 million usable fragments. 20-25 million is acceptable and < 15
    million is not compliant.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR999NKW
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: male adult (54 years)
    biosample_summary: Homo sapiens prostate gland tissue male adult (54 years)
    replication_type: unreplicated
    biosample_ontology: /biosample-types/tissue_UBERON_0002367/
    perturbed: false
    doi: 10.17989/ENCSR999NKW
    date_created: '2017-02-07T01:47:36.161360+00:00'
    date_released: '2017-06-21'
    submitter_comment: ''
