Resource
| Id | ATAC-seq/ENCSR863TVR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary |
ATAC-seq ENCSR863TVR [biosample_summary="Homo sapiens stimulated activated naive CD8-positive, alpha-beta T cell male adult (33 years) treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 100 ng/mL Interleukin-15 for 72 hours"]
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| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (33 years) treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 100 ng/mL Interleukin-15 for 72 hours output_type: pseudoreplicated peaks audit_error: Alignment file {ENCFF698LXZ|/files/ENCFF698LXZ/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 9618570 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 {ENCAN354YJJ|/analyses/ENCAN354YJJ/} 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 {ENCFF187EQF|/files/ENCFF187EQF/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.475579. 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 {ENCFF187EQF|/files/ENCFF187EQF/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.43. 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 {ENCFF698LXZ|/files/ENCFF698LXZ/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with NRF value of 0.298057. 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 {ENCFF698LXZ|/files/ENCFF698LXZ/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.22. audit_warning: Alignment file {ENCFF187EQF|/files/ENCFF187EQF/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 20481701 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_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 {ENCFF187EQF|/files/ENCFF187EQF/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC2 value of 1.51. 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 {ENCFF698LXZ|/files/ENCFF698LXZ/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with a PBC2 value of 1.10. audit_warning: 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. {ENCFF754SOL|/files/ENCFF754SOL/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has a FRiP score of 0.48. |
| Labels |
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Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| ATAC-seq_ENCSR863TVR | float |
ATAC-seq_ENCSR863TVR |
ATAC-seq ENCSR863TVR [biosample_summary="Homo sapiens stimulated activated naive CD8-positive, alpha-beta T cell male adult (33 years) treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 100 ng/mL Interleukin-15 for 72 hours"]
|
 |
[1.33, 38.8] |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF754SOL.bed.gz | 4.24 MB | 6c92ea00f17178ac438387e51c5b2ed7 |
| ENCFF754SOL.bed.gz.dvc | 101.0 B | 432745945a521422feac04cdae4bbefc |
| ENCFF754SOL.tabix.bed.gz | 1.09 MB | e341b1c897e80f02c8dd581e6a4737f4 |
| ENCFF754SOL.tabix.bed.gz.dvc | 107.0 B | 4ebeca691c4ebe12eb7bae83fd960cbe |
| ENCFF754SOL.tabix.bed.gz.tbi | 398.4 KB | d5bfa172ebe4778f62416eee359da4fd |
| ENCFF754SOL.tabix.bed.gz.tbi.dvc | 110.0 B | 06e84338579422582f3e14ca04034ff9 |
| genomic_resource.yaml | 6.94 KB | 991e9eb7d69b3e8dfe23c67715e88627 |
| statistics/ |