type: position_score
table:
  filename: ENCFF059YXD.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: TF_ChIP-seq_ENCSR000ALV
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000ALV [biosample_summary="Homo sapiens mammary epithelial cell female adult (50 years)" and target="CTCF"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000ALV [biosample_summary="Homo sapiens mammary epithelial cell female adult (50 years)" and target="CTCF"]'
  description: '**status**: released


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


    **summary**: female adult (50 years)


    **output\_type**: IDR thresholded peaks


    **audit\_error**: Processed alignments file {ENCFF472NHA|/files/ENCFF472NHA/}
    processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 4916002 usable fragments.
    The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    CTCF-human and investigated as a transcription factor is 10 million usable fragments.
    The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE
    ChIP-seq data standards|/data-standards/chip-seq/} )


    **audit\_internal\_action**: Released analysis {ENCAN429XCN|/analyses/ENCAN429XCN/}
    has in progress subobject document {52887bb2-dff6-4639-93be-2be188fc853c|/documents/52887bb2-dff6-4639-93be-2be188fc853c/}


    **audit\_internal\_action**: Released analysis {ENCAN429XCN|/analyses/ENCAN429XCN/}
    has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}


    **audit\_not\_compliant**: Processed alignments file {ENCFF086QJQ|/files/ENCFF086QJQ/}
    processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 9512981 usable fragments.
    The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    CTCF-human and investigated as a transcription factor is 10 million usable fragments.
    The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE
    ChIP-seq data standards|/data-standards/chip-seq/} )


    **audit\_warning**: 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 > 0.8 is acceptable. ENCODE processed alignments
    file {ENCFF086QJQ|/files/ENCFF086QJQ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.85.


    **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 alignments file {ENCFF086QJQ|/files/ENCFF086QJQ/}
    processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 6.35.


    **audit\_warning**: 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 > 0.8 is acceptable. ENCODE processed alignments
    file {ENCFF472NHA|/files/ENCFF472NHA/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.88.


    **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 alignments file {ENCFF472NHA|/files/ENCFF472NHA/}
    processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 8.76.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000ALV
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: female adult (50 years)
    biosample_summary: Homo sapiens mammary epithelial cell female adult (50 years)
    replication_type: isogenic
    biosample_ontology: /biosample-types/primary_cell_CL_0002327/
    perturbed: false
    doi: 10.17989/ENCSR000ALV
    date_created: '2013-11-07T22:16:23.952979+00:00'
    date_released: '2011-02-10'
    submitter_comment: There has been an error in running hg19.
    target: CTCF
