type: position_score
table:
  filename: ENCFF661VOO.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_ENCSR568PGX
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR568PGX [TISSUE: Homo sapiens K562, TARGET: HDAC1]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: optimal IDR thresholded peaks\n\n**audit\\\
    _internal\\_action**: Archived analysis {ENCAN261VAT|/analyses/ENCAN261VAT/} has\
    \ in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}\n\
    \n**audit\\_internal\\_action**: File {ENCFF661VOO|/files/ENCFF661VOO/} with status\
    \ 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status\
    \ 'archived'.\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 {ENCFF785NOU|/files/ENCFF785NOU/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ NRF value of 0.57.\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 {ENCFF785NOU|/files/ENCFF785NOU/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value\
    \ of 0.57.\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 {ENCFF785NOU|/files/ENCFF785NOU/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC2 value of 2.26.\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 {ENCFF135YTU|/files/ENCFF135YTU/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ NRF value of 0.75.\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 {ENCFF135YTU|/files/ENCFF135YTU/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value\
    \ of 0.75.\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 {ENCFF135YTU|/files/ENCFF135YTU/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC2 value of 3.87.\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 {ENCFF661VOO|/files/ENCFF661VOO/}, {ENCFF237ZFZ|/files/ENCFF237ZFZ/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 2.05 and\
    \ a self consistency ratio of 1.22. 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**: Replicate\
    \ concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible\
    \ Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF970LAU|/files/ENCFF970LAU/},\
    \ {ENCFF043QUA|/files/ENCFF043QUA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ have a rescue ratio of 2.05 and a self consistency ratio of 1.22. 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: ENCSR568PGX
    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/ENCSR568PGX
    date_created: '2016-04-29T17:08:31.765316+00:00'
    date_released: '2016-11-22'
    submitter_comment: Please note that the 'mixed platform' warning comes from the
      archived fastqs that were sequenced on the HiSeq2000 platform that if used,
      should be paired with the matching HiSeq2000 control ENCSR173USI. The pipeline
      was run on the fastqs and controls sequenced on the HiSeq4000 platform for consistency.
    target: HDAC1
