Histone_ChIP-seq_ENCSR000DQH
Histone_ChIP-seq ENCSR000DQH [biosample_summary="Homo sapiens BJ" and target="H3K4me3"]
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| Id: | Histone_ChIP-seq/ENCSR000DQH |
| Type: | position_score |
| Version: | 0 |
| Summary: |
HistoneChIP-seq ENCSR000DQH [biosamplesummary="Homo sapiens BJ" and target="H3K4me3"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN854KIB|/analyses/ENCAN854KIB/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF322CYX|/files/ENCFF322CYX/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 12776436 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 {ENCFF311CVR|/files/ENCFF311CVR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 10192374 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 {ENCFF322CYX|/files/ENCFF322CYX/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF322CYX|/files/ENCFF322CYX/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.33. 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 {ENCFF311CVR|/files/ENCFF311CVR/} 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 {ENCFF311CVR|/files/ENCFF311CVR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.72. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DQH | float |
Histone_ChIP-seq_ENCSR000DQH |
Histone_ChIP-seq ENCSR000DQH [biosample_summary="Homo sapiens BJ" and target="H3K4me3"]
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[1.86, 143] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF224GRF.bed.gz | 721.97 KB | 3ad908f9e79b4a6bd269af8c9a00f45d |
| ENCFF224GRF.bed.gz.dvc | 100.0 B | 0f62c30bba588321f51e38db6f1c4730 |
| ENCFF224GRF.tabix.bed.gz | 307.23 KB | 166c26d4a69ca7117ae3d53573c27da7 |
| ENCFF224GRF.tabix.bed.gz.dvc | 106.0 B | c6dae1116b344f140d7355c9d88bf9cd |
| ENCFF224GRF.tabix.bed.gz.tbi | 149.61 KB | 9aab618f55656e0237fa271058975dd5 |
| ENCFF224GRF.tabix.bed.gz.tbi.dvc | 110.0 B | d1f12711a614daac2bd81c2a6339b9d5 |
| genomic_resource.yaml | 4.95 KB | 12f2df98400c0fcb50a9c942aafbadc7 |
| genomic_resource_original.yaml | 4.84 KB | 00f019459a09f7d2a979897edc541c6b |
| statistics/ |