TF_ChIP-seq_ENCSR987MTA
TF_ChIP-seq ENCSR987MTA [biosample_summary="Homo sapiens GM12878" and target="BHLHE40"]
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| Id: | TF_ChIP-seq/ENCSR987MTA |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR987MTA [biosamplesummary="Homo sapiens GM12878" and target="BHLHE40"] |
| Description: |
status: released biological_replicates: Rep 4, Rep 5 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN408TIH|/analyses/ENCAN408TIH/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF431VZN|/files/ENCFF431VZN/} processed by ChIP-seq ENCODE3 hg19 pipeline has 19210865 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting BHLHE40-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/} ) 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 {ENCFF431VZN|/files/ENCFF431VZN/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.81. 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 {ENCFF431VZN|/files/ENCFF431VZN/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 5.26. 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 {ENCFF720VMA|/files/ENCFF720VMA/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF720VMA|/files/ENCFF720VMA/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.50. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF095GMM|/files/ENCFF095GMM/}, {ENCFF006MIL|/files/ENCFF006MIL/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.47 and a self consistency ratio of 2.02. 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. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF944MMI|/files/ENCFF944MMI/}, {ENCFF013NVT|/files/ENCFF013NVT/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.47 and a self consistency ratio of 2.02. 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: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR987MTA | float |
TF_ChIP-seq_ENCSR987MTA |
TF_ChIP-seq ENCSR987MTA [biosample_summary="Homo sapiens GM12878" and target="BHLHE40"]
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[9.22, 1.9e+04] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF095GMM.bed.gz | 883.69 KB | c23284256b4100cd845e6f844e468872 |
| ENCFF095GMM.bed.gz.dvc | 100.0 B | 8e09d95eb7bdb037d997c27b1f2f6490 |
| ENCFF095GMM.tabix.bed.gz | 619.99 KB | 2a5487815f95865cd6f03ed363d9817c |
| ENCFF095GMM.tabix.bed.gz.dvc | 106.0 B | 6bd63454a1611e90f2697186f5507137 |
| ENCFF095GMM.tabix.bed.gz.tbi | 249.31 KB | 41715076d39e7584e2ed54d88c6fb1e0 |
| ENCFF095GMM.tabix.bed.gz.tbi.dvc | 110.0 B | ddd173e9acee1bd80cd310cd9578c5c0 |
| genomic_resource.yaml | 5.58 KB | a22743b2b5ea04f4bd464e8b0bec52f9 |
| genomic_resource_original.yaml | 5.48 KB | cbc36380d149b1ff00665d1dcfdfe53e |
| statistics/ |