type: position_score
table:
  filename: ENCFF754SOL.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_ENCSR863TVR
  column_index: 3
  type: float
  desc: 'ATAC-seq ENCSR863TVR [biosample_summary="Homo sapiens stimulated activated naive CD8-positive, alpha-beta T cell male adult (33 years) treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 100 ng/mL Interleukin-15 for 72 hours"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR863TVR [biosample_summary="Homo sapiens stimulated activated naive CD8-positive, alpha-beta T cell male adult (33 years) treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 100 ng/mL Interleukin-15 for 72 hours"]'
  description: '**status**: released


    **biological\_replicates**: Rep 1, Rep 2


    **summary**: male adult (33 years) treated with anti-CD3 and anti-CD28 coated
    beads for 72 hours, 100 ng/mL Interleukin-15 for 72 hours


    **output\_type**: pseudoreplicated peaks


    **audit\_error**: Alignment file {ENCFF698LXZ|/files/ENCFF698LXZ/} processed by
    ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 9618570 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\_internal\_action**: Released analysis {ENCAN354YJJ|/analyses/ENCAN354YJJ/}
    has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}


    **audit\_not\_compliant**: 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 {ENCFF187EQF|/files/ENCFF187EQF/} processed
    by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with
    NRF value of 0.475579.


    **audit\_not\_compliant**: PBC1 (PCR Bottlenecking Coefficient 1, M1/M\_distinct)
    is the ratio of the number of genomic locations where  exactly one read maps uniquely
    (M1) to the number of genomic locations where some reads map (M\_distinct). A
    PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate
    bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking.
    PBC1 value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file
    {ENCFF187EQF|/files/ENCFF187EQF/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38
    pipeline was generated from a library with a PBC1 value of 0.43.


    **audit\_not\_compliant**: 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 {ENCFF698LXZ|/files/ENCFF698LXZ/} processed
    by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with
    NRF value of 0.298057.


    **audit\_not\_compliant**: PBC1 (PCR Bottlenecking Coefficient 1, M1/M\_distinct)
    is the ratio of the number of genomic locations where  exactly one read maps uniquely
    (M1) to the number of genomic locations where some reads map (M\_distinct). A
    PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate
    bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking.
    PBC1 value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file
    {ENCFF698LXZ|/files/ENCFF698LXZ/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38
    pipeline was generated from a library with a PBC1 value of 0.22.


    **audit\_warning**: Alignment file {ENCFF187EQF|/files/ENCFF187EQF/} processed
    by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 20481701 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\_warning**: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio
    of the number of genomic locations where exactly one read maps uniquely (M1) to
    the number of genomic locations where two reads map uniquely (M2). A PBC2 value
    in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3
    - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended,
    but > 3 is acceptable. ENCODE processed file {ENCFF187EQF|/files/ENCFF187EQF/}
    processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library
    with a PBC2 value of 1.51.


    **audit\_warning**: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio
    of the number of genomic locations where exactly one read maps uniquely (M1) to
    the number of genomic locations where two reads map uniquely (M2). A PBC2 value
    in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3
    - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended,
    but > 3 is acceptable. ENCODE processed file {ENCFF698LXZ|/files/ENCFF698LXZ/}
    processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library
    with a PBC2 value of 1.10.


    **audit\_warning**: 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. {ENCFF754SOL|/files/ENCFF754SOL/} processed by ATAC-seq
    ENCODE4 v1.10.0 GRCh38 pipeline  has a FRiP score of 0.48.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR863TVR
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: male adult (33 years) treated with anti-CD3 and anti-CD28
      coated beads for 72 hours, 100 ng/mL Interleukin-15 for 72 hours
    biosample_summary: Homo sapiens stimulated activated naive CD8-positive, alpha-beta
      T cell male adult (33 years) treated with anti-CD3 and anti-CD28 coated beads
      for 72 hours, 100 ng/mL Interleukin-15 for 72 hours
    replication_type: isogenic
    biosample_ontology: /biosample-types/primary_cell_NTR_0000667/
    perturbed: false
    doi: 10.17989/ENCSR863TVR
    date_created: '2021-09-22T22:30:52.501123+00:00'
    date_released: '2022-06-08'
    submitter_comment: This dataset has been released as part of a larger biosample
      and assay collection, despite noncompliance with ENCODE quality standards, due
      to lack of sample material to reattempt the assay.