type: position_score
table:
  filename: ENCFF718ZFY.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_ENCSR000EGQ
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR000EGQ [biosample_summary="Homo sapiens K562" and target="NFYB"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR000EGQ [biosample_summary="Homo sapiens K562" and target="NFYB"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: IDR thresholded peaks\n\n**audit\\_error**:\
    \ Processed alignments file {ENCFF737LSI|/files/ENCFF737LSI/} processed by ChIP-seq\
    \ ENCODE4 v1.6.1 GRCh38 pipeline has 3330017 usable fragments. The minimum ENCODE\
    \ standard for each replicate in a ChIP-seq experiment targeting NFYB-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\\_error**: Processed\
    \ alignments file {ENCFF981KIX|/files/ENCFF981KIX/} processed by ChIP-seq ENCODE4\
    \ v1.6.1 GRCh38 pipeline has 3653236 usable fragments. The minimum ENCODE standard\
    \ for each replicate in a ChIP-seq experiment targeting NFYB-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\\_internal\\_action**: Released\
    \ analysis {ENCAN131DRD|/analyses/ENCAN131DRD/} has in progress subobject document\
    \ {0403b388-375c-44d1-9898-4110c12e2a1f|/documents/0403b388-375c-44d1-9898-4110c12e2a1f/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN131DRD|/analyses/ENCAN131DRD/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\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 {ENCFF737LSI|/files/ENCFF737LSI/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with PBC1 value of 0.87.\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 {ENCFF737LSI|/files/ENCFF737LSI/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 7.79.\n\n**audit\\_warning**: 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 in the range 0 - 0.5 is poor\
    \ complexity, 0.5 - 0.8 is moderate complexity, and > 0.8 high complexity. NRF\
    \ value > 0.8 is recommended, but > 0.5 is acceptable. ENCODE processed alignments\
    \ file {ENCFF981KIX|/files/ENCFF981KIX/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with NRF value of 0.59.\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\
    \ {ENCFF981KIX|/files/ENCFF981KIX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38\
    \ pipeline was generated from a library with PBC1 value of 0.68.\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 {ENCFF981KIX|/files/ENCFF981KIX/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 3.60."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000EGQ
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens K562
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002067/
    perturbed: false
    doi: 10.17989/ENCSR000EGQ
    date_created: '2014-02-12T22:37:29.492539+00:00'
    date_released: '2011-10-29'
    submitter_comment: ''
    target: NFYB