Resource
| Id | ATAC-seq/ENCSR019XCN |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary |
ATAC-seq ENCSR019XCN [biosample_summary="Homo sapiens effector memory CD8-positive, alpha-beta T cell male adult (36 years)"]
|
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (36 years) output_type: pseudoreplicated peaks audit_error: Alignment file {ENCFF364RYN|/files/ENCFF364RYN/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 12745523 usable fragments. According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have > 25 million usable fragments. 20-25 million is acceptable and < 15 million is not compliant. audit_internal_action: Released analysis {ENCAN077FIR|/analyses/ENCAN077FIR/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_not_compliant: NRF (Non Redundant Fraction) is equal to the result of the division of the number of reads after duplicates removal by the total number of reads. An NRF value < 0.7 is poor complexity, between 0.7 and 0.9 is moderate complexity, and >= 0.9 high complexity. NRF value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF364RYN|/files/ENCFF364RYN/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.538814. audit_not_compliant: 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 > 0.7 is acceptable. ENCODE processed file {ENCFF364RYN|/files/ENCFF364RYN/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.50. audit_not_compliant: According to ENCODE4 standards, overlap peaks files in ATAC-seq assays processed by the uniform processing pipeline should have FRiP (fraction of reads in called peak regions) scores > 0.3. FRiP scores 0.2-0.3 are acceptable, and < 0.2 are not compliant. {ENCFF929NTI|/files/ENCFF929NTI/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has a FRiP score of 0.16. 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 file {ENCFF364RYN|/files/ENCFF364RYN/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC2 value of 1.78. audit_warning: NRF (Non Redundant Fraction) is equal to the result of the division of the number of reads after duplicates removal by the total number of reads. An NRF value < 0.7 is poor complexity, between 0.7 and 0.9 is moderate complexity, and >= 0.9 high complexity. NRF value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF347LNL|/files/ENCFF347LNL/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.833455. 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 > 0.7 is acceptable. ENCODE processed file {ENCFF347LNL|/files/ENCFF347LNL/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.83. audit_warning: According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have either >150k reproducible peaks in an overlap peaks file, or >70k in an IDR thresholded peaks file. 100-150k or 50-70k peaks respectively is acceptable, and <100k or <50k respectively is not compliant. File(s) {ENCFF929NTI|/files/ENCFF929NTI/} (overlap peaks) and {ENCFF603GBI|/files/ENCFF603GBI/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline have 89161 and 56932 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| ATAC-seq_ENCSR019XCN | float |
ATAC-seq_ENCSR019XCN |
ATAC-seq ENCSR019XCN [biosample_summary="Homo sapiens effector memory CD8-positive, alpha-beta T cell male adult (36 years)"]
|
 |
[1.41, 33.6] |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF929NTI.bed.gz | 2.14 MB | 695007603d004fcb8c9858f8e4b3702c |
| ENCFF929NTI.bed.gz.dvc | 101.0 B | ed58b1e24f0cced39bb7e22939ecbcb0 |
| ENCFF929NTI.tabix.bed.gz | 621.24 KB | 82065f2a9346df24b62c9bb6ff28fcf6 |
| ENCFF929NTI.tabix.bed.gz.dvc | 106.0 B | a0ebc73b0e787b50b3804ee14e7e0682 |
| ENCFF929NTI.tabix.bed.gz.tbi | 292.66 KB | 6814a92a58c2624faf9d22fe6df330d0 |
| ENCFF929NTI.tabix.bed.gz.tbi.dvc | 110.0 B | b848472866f72e94fa0d9a7b268f83c5 |
| genomic_resource.yaml | 5.96 KB | 2bba7bd92d0ab3761783c4cf173acb0f |
| statistics/ |