Histone_ChIP-seq_ENCSR000DVS
Histone_ChIP-seq ENCSR000DVS [biosample_summary="Homo sapiens fibroblast of villous mesenchyme" and target="H3K4me3"]
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| Id: | Histone_ChIP-seq/ENCSR000DVS |
| Type: | position_score |
| Version: | 0 |
| Summary: |
HistoneChIP-seq ENCSR000DVS [biosamplesummary="Homo sapiens fibroblast of villous mesenchyme" and target="H3K4me3"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN425MYE|/analyses/ENCAN425MYE/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF336RRY|/files/ENCFF336RRY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 18935038 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 {ENCFF398APA|/files/ENCFF398APA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 19621928 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 {ENCFF336RRY|/files/ENCFF336RRY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.82. 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 {ENCFF336RRY|/files/ENCFF336RRY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.19. 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 {ENCFF398APA|/files/ENCFF398APA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF398APA|/files/ENCFF398APA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.23. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DVS | float |
Histone_ChIP-seq_ENCSR000DVS |
Histone_ChIP-seq ENCSR000DVS [biosample_summary="Homo sapiens fibroblast of villous mesenchyme" and target="H3K4me3"]
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[1.88, 130] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF622AJL.bed.gz | 900.58 KB | 0f1b56f5e229eba2c1b2c61fe41f0834 |
| ENCFF622AJL.bed.gz.dvc | 100.0 B | 6c5194895b2c433f9012c4c6ee73a2e8 |
| ENCFF622AJL.tabix.bed.gz | 399.51 KB | de10abf6c050ab647e97828ac006e698 |
| ENCFF622AJL.tabix.bed.gz.dvc | 106.0 B | 63de70f2b72f3d91a174a3ae0e5b03b2 |
| ENCFF622AJL.tabix.bed.gz.tbi | 183.22 KB | 5c720b21f89286e63384540360847795 |
| ENCFF622AJL.tabix.bed.gz.tbi.dvc | 110.0 B | 7db6f9bcacdd5794947eeb57ae0cedec |
| genomic_resource.yaml | 5.04 KB | 1988524040214f6fe52c0347b15e1d68 |
| genomic_resource_original.yaml | 4.91 KB | e0a1d6ec9678c8392e4b4ab8be508a28 |
| statistics/ |