| Id: | TF_ChIP-seq/ENCSR602QEJ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR602QEJ [biosamplesummary="Homo sapiens SK-N-SH genetically modified\ \ (insertion) using CRISPR targeting H. sapiens PPARA treated with 6 \u03BCM all-trans-retinoic\ \ acid for 48 hours" and target="PPARA"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: treated with 6 μM all-trans-retinoic acid for 48 hours genetically modified (insertion) using CRISPR targeting H. sapiens PPARA output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN950BMU|/analyses/ENCAN950BMU/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_internal_action: Released analysis {ENCAN950BMU|/analyses/ENCAN950BMU/} has in progress subobject document {1681b2ec-8d11-4974-9621-94ed09de8801|/documents/1681b2ec-8d11-4974-9621-94ed09de8801/} 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 {ENCFF120BHB|/files/ENCFF120BHB/} processed by ChIP-seq ENCODE4 v1.5.0 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 {ENCFF120BHB|/files/ENCFF120BHB/} processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline was generated from a library with PBC2 value of 6.80. 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 {ENCFF014HOC|/files/ENCFF014HOC/} processed by ChIP-seq ENCODE4 v1.5.0 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 {ENCFF014HOC|/files/ENCFF014HOC/} processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline was generated from a library with PBC2 value of 6.64. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF708MEQ|/files/ENCFF708MEQ/} processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline have a rescue ratio of 1.09 and a self consistency ratio of 2.17. 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 {ENCFF446HWC|/files/ENCFF446HWC/} processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline have a rescue ratio of 1.09 and a self consistency ratio of 2.17. 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_ENCSR602QEJ | float |
TF_ChIP-seq_ENCSR602QEJ |
TF_ChIP-seq ENCSR602QEJ [biosample_summary="Homo sapiens SK-N-SH genetically modified\ \ (insertion) using CRISPR targeting H. sapiens PPARA treated with 6 \u03BCM all-trans-retinoic\ \ acid for 48 hours" and target="PPARA"]
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[12.9, 552] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF708MEQ.bed.gz | 26.8 KB | 287d8d2f8cdb7c9a984ea9a41f612b4d |
| ENCFF708MEQ.bed.gz.dvc | 99.0 B | f071b69d4ce5fbb5b3643b3a3cbe7bb4 |
| ENCFF708MEQ.tabix.bed.gz | 16.88 KB | f8d930fc9d334c99c1e33433e7ea3604 |
| ENCFF708MEQ.tabix.bed.gz.dvc | 105.0 B | 379d15f81671c4d4843e8fabc070ca3b |
| ENCFF708MEQ.tabix.bed.gz.tbi | 18.17 KB | fbcc6ce3498867bf6eb32d9d3c96c284 |
| ENCFF708MEQ.tabix.bed.gz.tbi.dvc | 109.0 B | 5d3fb14826392a265aedb1b5997b9ef4 |
| genomic_resource.yaml | 5.98 KB | 674b3ff6e096f5baae703ada9680e1cd |
| genomic_resource_original.yaml | 5.75 KB | b4ecf0804ff5d0c4d547cb7782ea3e6b |
| statistics/ |