TF_ChIP-seq_ENCSR000DOC
TF_ChIP-seq ENCSR000DOC [biosample_summary="Homo sapiens K562" and target="BRF2"]
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| Id: | TF_ChIP-seq/ENCSR000DOC |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000DOC [biosamplesummary="Homo sapiens K562" and target="BRF2"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2, Rep 3 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN992PCZ|/analyses/ENCAN992PCZ/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_internal_action: Released analysis {ENCAN992PCZ|/analyses/ENCAN992PCZ/} has in progress subobject document {bb36280b-29a3-48ea-b7e0-99675e1a8c95|/documents/bb36280b-29a3-48ea-b7e0-99675e1a8c95/} audit_not_compliant: Processed alignments file {ENCFF451HJD|/files/ENCFF451HJD/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 5968957 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting BRF2-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_not_compliant: Processed alignments file {ENCFF228MIZ|/files/ENCFF228MIZ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 6350146 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting BRF2-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_not_compliant: Processed alignments file {ENCFF774PJX|/files/ENCFF774PJX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 5455718 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting BRF2-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 {ENCFF774PJX|/files/ENCFF774PJX/} 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 {ENCFF774PJX|/files/ENCFF774PJX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.21. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF944LWS|/files/ENCFF944LWS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 1.34 and a self consistency ratio of 2.58. 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_ENCSR000DOC | float |
TF_ChIP-seq_ENCSR000DOC |
TF_ChIP-seq ENCSR000DOC [biosample_summary="Homo sapiens K562" and target="BRF2"]
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[8.28, 194] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF944LWS.bed.gz | 984.0 B | 00950d75f1fefb8f08d6f3b6772b0428 |
| ENCFF944LWS.bed.gz.dvc | 97.0 B | 8423affe034cba64568399507fc095c2 |
| ENCFF944LWS.tabix.bed.gz | 669.0 B | 9a05ec86178c226c8d7fb342dcc1a4f5 |
| ENCFF944LWS.tabix.bed.gz.dvc | 103.0 B | 83a3332ba1920950ed738ea9505e64ec |
| ENCFF944LWS.tabix.bed.gz.tbi | 2.53 KB | 08d8f95e66b53be070dba728373aab67 |
| ENCFF944LWS.tabix.bed.gz.tbi.dvc | 108.0 B | 64547aaa4355d1d0228c0fe929151a15 |
| genomic_resource.yaml | 4.94 KB | 3b757d86de3fd216d5a8a53e828da7df |
| genomic_resource_original.yaml | 4.85 KB | a09e13ce345ef5fed8b7c796b9400a16 |
| statistics/ |