ATAC-seq_ENCSR851SBY
ATAC-seq ENCSR851SBY [biosample_summary="Homo sapiens stomach tissue male adult (54 years)"]
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| Id: | ATAC-seq/ENCSR851SBY |
| Type: | position_score |
| Version: | 0 |
| Summary: |
ATAC-seq ENCSR851SBY [biosample_summary="Homo sapiens stomach tissue male adult (54 years)"] |
| Description: |
status: released biological_replicates: Rep 1 summary: male adult (54 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN924FND|/analyses/ENCAN924FND/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN924FND|/analyses/ENCAN924FND/} has in progress subobject document {f73153a5-f608-49c9-9325-08cc6157d579|/documents/f73153a5-f608-49c9-9325-08cc6157d579/} 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. {ENCFF028CAI|/files/ENCFF028CAI/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.09. 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 {ENCFF858TZP|/files/ENCFF858TZP/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.881097. 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 {ENCFF858TZP|/files/ENCFF858TZP/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.89. 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) {ENCFF028CAI|/files/ENCFF028CAI/} (overlap peaks) and {ENCFF430VEQ|/files/ENCFF430VEQ/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 103609 and 48990 peaks. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| ATAC-seq_ENCSR851SBY | float |
ATAC-seq_ENCSR851SBY |
ATAC-seq ENCSR851SBY [biosample_summary="Homo sapiens stomach tissue male adult (54 years)"]
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[1.47, 29.8] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF028CAI.bed.gz | 2.48 MB | 60a1926a8abb58c8943f5a66a9215d62 |
| ENCFF028CAI.bed.gz.dvc | 101.0 B | 9c5172243052ac9a251541432022f77b |
| ENCFF028CAI.tabix.bed.gz | 755.19 KB | 73aaed44f3daf2ac61d0f78a16c6ae66 |
| ENCFF028CAI.tabix.bed.gz.dvc | 106.0 B | 838d361251f89b5cd9120050ae93a3a3 |
| ENCFF028CAI.tabix.bed.gz.tbi | 345.01 KB | 42c5e1ac4b95ddacf98a1eac8beb6e8d |
| ENCFF028CAI.tabix.bed.gz.tbi.dvc | 110.0 B | 4cc8fbc6aa1a6fc9c4d8fa2c1f5f37df |
| genomic_resource.yaml | 3.72 KB | 57d581678ada85479425c5b6e6052d4d |
| genomic_resource_original.yaml | 3.62 KB | 443092b1678ad13f1b4ccd1894eda4f3 |
| statistics/ |