TF_ChIP-seq_ENCSR836COE
TF_ChIP-seq ENCSR836COE [biosample_summary="Homo sapiens K562" and target="RBM17"]
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| Id: | TF_ChIP-seq/ENCSR836COE |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR836COE [biosamplesummary="Homo sapiens K562" and target="RBM17"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN390ZQK|/analyses/ENCAN390ZQK/} has in progress subobject document {fb988828-bc7a-4627-a5a4-16aae37656ad|/documents/fb988828-bc7a-4627-a5a4-16aae37656ad/} audit_internal_action: Released analysis {ENCAN390ZQK|/analyses/ENCAN390ZQK/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF557XCY|/files/ENCFF557XCY/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 12203056 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting RBM17-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: Processed alignments file {ENCFF066QWS|/files/ENCFF066QWS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 11140303 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting RBM17-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 {ENCFF557XCY|/files/ENCFF557XCY/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF557XCY|/files/ENCFF557XCY/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.36. 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 {ENCFF066QWS|/files/ENCFF066QWS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF066QWS|/files/ENCFF066QWS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.24. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF937QYU|/files/ENCFF937QYU/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 1.55 and a self consistency ratio of 2.33. 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_ENCSR836COE | float |
TF_ChIP-seq_ENCSR836COE |
TF_ChIP-seq ENCSR836COE [biosample_summary="Homo sapiens K562" and target="RBM17"]
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[6.06, 47.2] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF937QYU.bed.gz | 1.06 KB | 1a6b77eb0e96a0230811eec34f82fa0b |
| ENCFF937QYU.bed.gz.dvc | 98.0 B | 13b9af0820149e2f09853fc059e35e3a |
| ENCFF937QYU.tabix.bed.gz | 810.0 B | 5deb2ad71b0ef374f8c25640ba24d723 |
| ENCFF937QYU.tabix.bed.gz.dvc | 103.0 B | 0eb47bb3505840b3268e590526bab329 |
| ENCFF937QYU.tabix.bed.gz.tbi | 1.65 KB | 677b8da41857c0579f2a22bc70921cbd |
| ENCFF937QYU.tabix.bed.gz.tbi.dvc | 108.0 B | d04bc26592a716043ff9224372f5d974 |
| genomic_resource.yaml | 5.73 KB | 6c99a9fe14ac6ec261aad58ee8666441 |
| genomic_resource_original.yaml | 5.64 KB | 47485342ae535c88de62ea6cf3a3f2e1 |
| statistics/ |