type: position_score table: filename: ENCFF991VQQ.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: Histone_ChIP-seq_ENCSR000DPR column_index: 3 type: float desc: signal histogram: type: number number_of_bins: 100 meta: summary: 'ChIP-seq ENCSR000DPR [TISSUE: Homo sapiens AG09309, TARGET: H3K4me3]' description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\ \n**summary**: \n\n**output\\_type**: replicated peaks\n\n**audit\\_internal\\\ _action**: Archived analysis {ENCAN713RXU|/analyses/ENCAN713RXU/} has in progress\ \ subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/}\n\ \n**audit\\_warning**: Processed alignments file {ENCFF464ZQX|/files/ENCFF464ZQX/}\ \ processed by ChIP-seq ENCODE3 hg19 pipeline has 14226836 usable fragments. The\ \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\ \ H3K4me3-human and investigated as a narrow histone mark 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 {ENCFF705CYF|/files/ENCFF705CYF/} processed\ \ by ChIP-seq ENCODE3 hg19 pipeline has 18518123 usable fragments. The minimum\ \ ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human\ \ and investigated as a narrow histone mark 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**:\ \ 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 {ENCFF464ZQX|/files/ENCFF464ZQX/} processed\ \ by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with NRF value\ \ of 0.79.\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 {ENCFF464ZQX|/files/ENCFF464ZQX/} processed by ChIP-seq\ \ ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.81.\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 {ENCFF464ZQX|/files/ENCFF464ZQX/}\ \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\ \ PBC2 value of 5.77.\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 {ENCFF705CYF|/files/ENCFF705CYF/} processed by ChIP-seq ENCODE3 hg19 pipeline\ \ was generated from a library with NRF value of 0.71.\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\ \ {ENCFF705CYF|/files/ENCFF705CYF/} processed by ChIP-seq ENCODE3 hg19 pipeline\ \ was generated from a library with PBC1 value of 0.73.\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 {ENCFF705CYF|/files/ENCFF705CYF/}\ \ processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with\ \ PBC2 value of 4.20." labels: reference_genome: hg38/genomes/GRCh38-hg38 accession: ENCSR000DPR status: released assay_term_name: ChIP-seq simple_biosample_summary: '' biosample_summary: Homo sapiens AG09309 replication_type: isogenic biosample_ontology: /biosample-types/cell_line_CLO_0021752/ perturbed: false doi: 10.17989/ENCSR000DPR date_created: '2014-02-12T23:06:14.339027+00:00' date_released: '2011-02-11' submitter_comment: Replicate 1,1 of this experiment was previously attributed to biosample ENCBS005ENC and replicate 2,1 of this experiment was previously attributed to biosample ENCBS005ENC but they have since been corrected to the current biosamples. Please note that the biosample term has remain unchanged. target: H3K4me3