type: position_score
table:
  filename: ENCFF358XFJ.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_ENCSR000BJJ
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR000BJJ [TISSUE: Homo sapiens SK-N-SH, TARGET: REST]'
  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 {ENCAN120BZI|/analyses/ENCAN120BZI/} has in progress\
    \ subobject document {35f4af5f-3e14-482f-bb41-dbd1fd1524a7|/documents/35f4af5f-3e14-482f-bb41-dbd1fd1524a7/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN120BZI|/analyses/ENCAN120BZI/}\
    \ 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 {ENCFF358XFJ|/files/ENCFF358XFJ/} processed by ChIP-seq\
    \ ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 3.68 and a self consistency\
    \ ratio of 5.56. 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\
    \ {ENCFF310DLW|/files/ENCFF310DLW/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38\
    \ pipeline has 10566392 usable fragments. The minimum ENCODE standard for each\
    \ replicate in a ChIP-seq experiment targeting REST-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 {ENCFF155PZC|/files/ENCFF155PZC/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline has 13651188 usable fragments. The minimum ENCODE standard for\
    \ each replicate in a ChIP-seq experiment targeting REST-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/} )"
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000BJJ
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens SK-N-SH
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0003072/
    perturbed: false
    doi: 10.17989/ENCSR000BJJ
    date_created: '2013-09-13T15:59:18.270610-08:00'
    date_released: '2011-07-18'
    submitter_comment: 'Fastq file ENCFF000RAL contains reads of mixed lengths. Read
      lengths followed by respective number of reads: (32, 3972256), (36, 31246798).'
    target: REST
