type: position_score table: filename: ENCFF684BIN.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_ENCSR000DNP column_index: 3 type: float desc: 'TF_ChIP-seq ENCSR000DNP [biosample_summary="Homo sapiens GM12878" and target="SUPT20H"]' histogram: type: number number_of_bins: 100 meta: summary: 'TF_ChIP-seq ENCSR000DNP [biosample_summary="Homo sapiens GM12878" and target="SUPT20H"]' 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 {ENCAN456BBZ|/analyses/ENCAN456BBZ/} has in progress\ \ subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\ \n**audit\\_warning**: Processed alignments file {ENCFF359GVP|/files/ENCFF359GVP/}\ \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 15260566 usable fragments.\ \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\ \ SUPT20H-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 {ENCFF345ORP|/files/ENCFF345ORP/} processed\ \ by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 17494498 usable fragments. The\ \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\ \ SUPT20H-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**: 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 {ENCFF359GVP|/files/ENCFF359GVP/}\ \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 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 {ENCFF359GVP|/files/ENCFF359GVP/} processed\ \ by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with\ \ PBC1 value of 0.78.\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 {ENCFF359GVP|/files/ENCFF359GVP/} processed by ChIP-seq ENCODE4 v1.6.1\ \ GRCh38 pipeline was generated from a library with PBC2 value of 4.30.\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\ \ {ENCFF345ORP|/files/ENCFF345ORP/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38\ \ pipeline was generated from a library with PBC1 value of 0.85.\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 {ENCFF345ORP|/files/ENCFF345ORP/}\ \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\ \ with PBC2 value of 6.28.\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 {ENCFF684BIN|/files/ENCFF684BIN/}\ \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of\ \ 1.23 and a self consistency ratio of 2.81. 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: ENCSR000DNP status: released assay_term_name: ChIP-seq simple_biosample_summary: '' biosample_summary: Homo sapiens GM12878 replication_type: isogenic biosample_ontology: /biosample-types/cell_line_EFO_0002784/ perturbed: false doi: 10.17989/ENCSR000DNP date_created: '2014-02-12T23:28:19.158897+00:00' date_released: '2011-10-29' submitter_comment: The data quality is too poor for peak analysis for hg19. Not enough peaks can be called. The GRCh38 data should also be used with caution. target: SUPT20H