type: position_score
table:
  filename: ENCFF496SMN.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_ENCSR872EVQ
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR872EVQ [TISSUE: Homo sapiens HepG2, TARGET: PCBP1]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: IDR thresholded peaks\n\n**audit\\_internal\\\
    _action**: Released analysis {ENCAN962MPL|/analyses/ENCAN962MPL/} has in progress\
    \ subobject document {98a1dd87-a227-4ae9-9eb9-15560674c7fb|/documents/98a1dd87-a227-4ae9-9eb9-15560674c7fb/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN962MPL|/analyses/ENCAN962MPL/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_warning**: Processed alignments file {ENCFF780OJV|/files/ENCFF780OJV/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 11148548 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ PCBP1-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/} )\n\n**audit\\\
    _warning**: Processed alignments file {ENCFF146SVH|/files/ENCFF146SVH/} processed\
    \ by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 10944397 usable fragments. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ PCBP1-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/} )\n\n**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\
    \ {ENCFF146SVH|/files/ENCFF146SVH/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38\
    \ pipeline was generated from a library with PBC1 value of 0.86.\n\n**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 {ENCFF146SVH|/files/ENCFF146SVH/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 6.87.\n\n**audit\\_warning**: Replicate concordance in ChIP-seq\
    \ experiments is measured by calculating IDR values (Irreproducible Discovery\
    \ Rate). ENCODE processed IDR thresholded peaks files {ENCFF496SMN|/files/ENCFF496SMN/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of\
    \ 1.03 and a self consistency ratio of 2.03. According to ENCODE standards, having\
    \ both rescue ratio and self consistency ratio values < 2 is recommended, but\
    \ having only one of the ratio values < 2 is acceptable."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR872EVQ
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens HepG2
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0001187/
    perturbed: false
    doi: 10.17989/ENCSR872EVQ
    date_created: '2017-01-25T23:24:41.602534+00:00'
    date_released: '2017-02-27'
    submitter_comment: ''
    target: PCBP1