Histone_ChIP-seq_ENCSR000DRY
Histone_ChIP-seq ENCSR000DRY [biosample_summary="Homo sapiens GM12878" and target="H3K4me3"]
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| Id: | Histone_ChIP-seq/ENCSR000DRY |
| Type: | position_score |
| Version: | 0 |
| Summary: |
HistoneChIP-seq ENCSR000DRY [biosamplesummary="Homo sapiens GM12878" and target="H3K4me3"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN413OBZ|/analyses/ENCAN413OBZ/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF822SQU|/files/ENCFF822SQU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 14556240 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/}) audit_warning: Processed alignments file {ENCFF147ZCK|/files/ENCFF147ZCK/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 17411006 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/}) 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 {ENCFF822SQU|/files/ENCFF822SQU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF822SQU|/files/ENCFF822SQU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.80. 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 {ENCFF147ZCK|/files/ENCFF147ZCK/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. 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 {ENCFF147ZCK|/files/ENCFF147ZCK/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.92. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DRY | float |
Histone_ChIP-seq_ENCSR000DRY |
Histone_ChIP-seq ENCSR000DRY [biosample_summary="Homo sapiens GM12878" and target="H3K4me3"]
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[1.87, 88.6] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF636FWF.bed.gz | 964.66 KB | b15fe763b45e6ee0e473927caa1cec64 |
| ENCFF636FWF.bed.gz.dvc | 100.0 B | bb4b3c22355bb6e7045b199bf7064e9c |
| ENCFF636FWF.tabix.bed.gz | 439.53 KB | 47871922783945078742065951c447f3 |
| ENCFF636FWF.tabix.bed.gz.dvc | 106.0 B | 75c0e042378e50979eef8c8d1509b773 |
| ENCFF636FWF.tabix.bed.gz.tbi | 136.73 KB | 534e91de38bd9cd5e960bbc46e5a08c4 |
| ENCFF636FWF.tabix.bed.gz.tbi.dvc | 110.0 B | c22eb9a72bd74d9a346a9f3ffd826957 |
| genomic_resource.yaml | 5.26 KB | fab92c76497f49e4981bbc305e8b14fc |
| genomic_resource_original.yaml | 5.15 KB | 40af93a9358812aeb0420a91e39e0b32 |
| statistics/ |