TF_ChIP-seq_ENCSR000EFI
TF_ChIP-seq ENCSR000EFI [biosample_summary="Homo sapiens IMR-90" and target="CTCF"]
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| Id: | TF_ChIP-seq/ENCSR000EFI |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000EFI [biosamplesummary="Homo sapiens IMR-90" and target="CTCF"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: File {ENCFF307XFM|/files/ENCFF307XFM/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_internal_action: Archived analysis {ENCAN816KVY|/analyses/ENCAN816KVY/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF431WUY|/files/ENCFF431WUY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 15370454 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 {ENCFF010FWV|/files/ENCFF010FWV/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 16593068 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 {ENCFF431WUY|/files/ENCFF431WUY/} processed by ChIP-seq ENCODE3 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 {ENCFF431WUY|/files/ENCFF431WUY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.54. 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 {ENCFF010FWV|/files/ENCFF010FWV/} processed by ChIP-seq ENCODE3 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 {ENCFF010FWV|/files/ENCFF010FWV/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.39. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000EFI | float |
TF_ChIP-seq_ENCSR000EFI |
TF_ChIP-seq ENCSR000EFI [biosample_summary="Homo sapiens IMR-90" and target="CTCF"]
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[3.81, 584] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF307XFM.bed.gz | 732.3 KB | f60418b9e2d782a74e0696aaeaa1c570 |
| ENCFF307XFM.bed.gz.dvc | 100.0 B | 857d51656c28d2885cf38325ed473e29 |
| ENCFF307XFM.tabix.bed.gz | 530.04 KB | 816ce63c7b021edda3bc426aef2dea78 |
| ENCFF307XFM.tabix.bed.gz.dvc | 106.0 B | 67e981e802cf3f9cc2587a8cf2b0f92f |
| ENCFF307XFM.tabix.bed.gz.tbi | 278.51 KB | a22f7031554ff344d62b2356758e3422 |
| ENCFF307XFM.tabix.bed.gz.tbi.dvc | 110.0 B | 7b7547b08cb7f8664da96ad2f818d05c |
| genomic_resource.yaml | 5.12 KB | cc92d72363461244c8c63c412a9f28d9 |
| genomic_resource_original.yaml | 5.03 KB | 45ba365bd5acd01db23b33a41063a4d8 |
| statistics/ |