type: position_score
table:
  filename: ENCFF818EYD.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_ENCSR647AOY
  column_index: 3
  type: float
  desc: 'ATAC-seq ENCSR647AOY [biosample_summary="Homo sapiens lung tissue female adult (47 years)"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR647AOY [biosample_summary="Homo sapiens lung tissue female adult (47 years)"]'
  description: '**status**: released


    **biological\_replicates**: Rep 1


    **summary**: female adult (47 years)


    **output\_type**: pseudoreplicated peaks


    **audit\_internal\_action**: Released analysis {ENCAN079QLM|/analyses/ENCAN079QLM/}
    has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}


    **audit\_internal\_action**: Released analysis {ENCAN079QLM|/analyses/ENCAN079QLM/}
    has in progress subobject document {50503732-021d-48d5-992a-6017f3c3ef03|/documents/50503732-021d-48d5-992a-6017f3c3ef03/}


    **audit\_not\_compliant**: Alignment file {ENCFF810ZGD|/files/ENCFF810ZGD/} processed
    by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 18425763 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.


    **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. {ENCFF818EYD|/files/ENCFF818EYD/} processed
    by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline  has a FRiP score of 0.18.


    **audit\_warning**: 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) {ENCFF818EYD|/files/ENCFF818EYD/} (overlap peaks) and {ENCFF068ZZZ|/files/ENCFF068ZZZ/}
    (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have
    107260 and 48163 peaks.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR647AOY
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: female adult (47 years)
    biosample_summary: Homo sapiens lung tissue female adult (47 years)
    replication_type: unreplicated
    biosample_ontology: /biosample-types/tissue_UBERON_0002048/
    perturbed: false
    doi: 10.17989/ENCSR647AOY
    date_created: '2019-07-30T07:15:39.079025+00:00'
    date_released: '2020-07-21'
    submitter_comment: ''