TF_ChIP-seq_ENCSR013UDY
TF_ChIP-seq ENCSR013UDY [biosample_summary="Homo sapiens K562 genetically modified (insertion) using CRISPR targeting H. sapiens TOE1" and target="TOE1"]
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| Id: | TF_ChIP-seq/ENCSR013UDY |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR013UDY [biosamplesummary="Homo sapiens K562 genetically modified (insertion) using CRISPR targeting H. sapiens TOE1" and target="TOE1"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: genetically modified (insertion) using CRISPR targeting H. sapiens TOE1 output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN396RAA|/analyses/ENCAN396RAA/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF664VBD|/files/ENCFF664VBD/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline has 19238511 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting TOE1-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 {ENCFF664VBD|/files/ENCFF664VBD/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF664VBD|/files/ENCFF664VBD/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC2 value of 7.82. 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 {ENCFF420EPJ|/files/ENCFF420EPJ/} processed by ChIP-seq ENCODE4 v1.8.0 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 {ENCFF420EPJ|/files/ENCFF420EPJ/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC2 value of 5.97. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF917HUH|/files/ENCFF917HUH/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline have a rescue ratio of 1.07 and a self consistency ratio of 2.01. 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_ENCSR013UDY | float |
TF_ChIP-seq_ENCSR013UDY |
TF_ChIP-seq ENCSR013UDY [biosample_summary="Homo sapiens K562 genetically modified (insertion) using CRISPR targeting H. sapiens TOE1" and target="TOE1"]
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[8.6, 339] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF917HUH.bed.gz | 76.79 KB | 028d5e474d612dda1bb14321bd71113d |
| ENCFF917HUH.bed.gz.dvc | 99.0 B | d8c5188e43440eb2d79f74bede5ec6b8 |
| ENCFF917HUH.tabix.bed.gz | 52.89 KB | 693f253a649fe532551ff780c79daf5d |
| ENCFF917HUH.tabix.bed.gz.dvc | 105.0 B | 49eb9d25dd2183a922b137175746a44a |
| ENCFF917HUH.tabix.bed.gz.tbi | 34.48 KB | 548ccc6862353da9f7d0a9d5e69cb446 |
| ENCFF917HUH.tabix.bed.gz.tbi.dvc | 109.0 B | 88e8723762c321c932a7b1e086d5b60b |
| genomic_resource.yaml | 5.22 KB | 2a9b8ae5d7aa3d53b94cd67ee048c8a1 |
| genomic_resource_original.yaml | 5.06 KB | 5ad0006d0802fddac891f1c34b73dc0e |
| statistics/ |