TF_ChIP-seq_ENCSR000DLB
TF_ChIP-seq ENCSR000DLB [biosample_summary="Homo sapiens GM13977" and target="CTCF"]
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| Id: | TF_ChIP-seq/ENCSR000DLB |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000DLB [biosamplesummary="Homo sapiens GM13977" and target="CTCF"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN375BDX|/analyses/ENCAN375BDX/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF075LLZ|/files/ENCFF075LLZ/} processed by ChIP-seq ENCODE3 hg19 pipeline has 8320360 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-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 {ENCFF370KVW|/files/ENCFF370KVW/} processed by ChIP-seq ENCODE3 hg19 pipeline has 16233023 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-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 {ENCFF370KVW|/files/ENCFF370KVW/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF370KVW|/files/ENCFF370KVW/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 9.69. 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 {ENCFF075LLZ|/files/ENCFF075LLZ/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF075LLZ|/files/ENCFF075LLZ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 9.29. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000DLB | float |
TF_ChIP-seq_ENCSR000DLB |
TF_ChIP-seq ENCSR000DLB [biosample_summary="Homo sapiens GM13977" and target="CTCF"]
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[4.21, 345] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF445ATY.bed.gz | 733.24 KB | 9cb6f944b978f18fb4831d56fa835b97 |
| ENCFF445ATY.bed.gz.dvc | 100.0 B | 587e18dec04e48f5e502e825fdc5525a |
| ENCFF445ATY.tabix.bed.gz | 551.2 KB | 186ec6dc3f7de079186692689fff70d5 |
| ENCFF445ATY.tabix.bed.gz.dvc | 106.0 B | 52ed0b482af41570b72bd108f71fbe19 |
| ENCFF445ATY.tabix.bed.gz.tbi | 288.26 KB | f3cc6404d5d7b072c005cdc694de7c15 |
| ENCFF445ATY.tabix.bed.gz.tbi.dvc | 110.0 B | a3ef55f1d6cfaa430d8fc992d9c40dee |
| genomic_resource.yaml | 4.94 KB | 953192d6e599e17ecc3701be9e7f2614 |
| genomic_resource_original.yaml | 4.84 KB | 67feab9e6c4e1d1aeee8f3a9b62de268 |
| statistics/ |