type: position_score
table:
  filename: ENCFF806TIM.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_ENCSR000BJX
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR000BJX [TISSUE: Homo sapiens HepG2, TARGET: SP1]'
  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 {ENCAN029VQS|/analyses/ENCAN029VQS/} has in progress\
    \ subobject document {1c22705b-d200-491d-ae6e-fa64bb049aa9|/documents/1c22705b-d200-491d-ae6e-fa64bb049aa9/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN029VQS|/analyses/ENCAN029VQS/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_not\\_compliant**: Replicate concordance in ChIP-seq experiments is\
    \ measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed\
    \ IDR thresholded peaks files {ENCFF806TIM|/files/ENCFF806TIM/} processed by ChIP-seq\
    \ ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 11.84 and a self consistency\
    \ ratio of 86.47. 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.\n\n**audit\\_warning**: Processed alignments\
    \ file {ENCFF718SND|/files/ENCFF718SND/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline has 17793239 usable fragments. The minimum ENCODE standard for\
    \ each replicate in a ChIP-seq experiment targeting SP1-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 {ENCFF241ZKB|/files/ENCFF241ZKB/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline has 12139668 usable fragments. The minimum ENCODE standard for\
    \ each replicate in a ChIP-seq experiment targeting SP1-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 {ENCFF241ZKB|/files/ENCFF241ZKB/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC1 value of 0.89.\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 {ENCFF241ZKB|/files/ENCFF241ZKB/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 8.68."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000BJX
    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/ENCSR000BJX
    date_created: '2013-09-13T15:57:46.617340-08:00'
    date_released: '2011-07-18'
    submitter_comment: ''
    target: SP1