ATAC-seq_ENCSR373TDL
ATAC-seq ENCSR373TDL [biosample_summary="Homo sapiens right lobe of liver tissue female adult (53 years)"]
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| Id: | ATAC-seq/ENCSR373TDL |
| Type: | position_score |
| Version: | 0 |
| Summary: |
ATAC-seq ENCSR373TDL [biosample_summary="Homo sapiens right lobe of liver tissue female adult (53 years)"] |
| Description: |
status: released biological_replicates: Rep 1 summary: female adult (53 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN907OKQ|/analyses/ENCAN907OKQ/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN907OKQ|/analyses/ENCAN907OKQ/} has in progress subobject document {f217c95d-6106-41a8-b512-046998322662|/documents/f217c95d-6106-41a8-b512-046998322662/} 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. {ENCFF360SWK|/files/ENCFF360SWK/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.08. 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 {ENCFF205LVV|/files/ENCFF205LVV/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.872159. 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 {ENCFF205LVV|/files/ENCFF205LVV/} 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) {ENCFF360SWK|/files/ENCFF360SWK/} (overlap peaks) and {ENCFF522FNJ|/files/ENCFF522FNJ/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 104179 and 39822 peaks. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| ATAC-seq_ENCSR373TDL | float |
ATAC-seq_ENCSR373TDL |
ATAC-seq ENCSR373TDL [biosample_summary="Homo sapiens right lobe of liver tissue female adult (53 years)"]
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[1.66, 30.4] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF360SWK.bed.gz | 2.42 MB | 58df987dbd2c8853a378b7102cc99198 |
| ENCFF360SWK.bed.gz.dvc | 101.0 B | 3a914dbbcb7f7f67354e3ce960b8cf53 |
| ENCFF360SWK.tabix.bed.gz | 824.78 KB | aa7881c84f3c6f48759ba95f2e66632f |
| ENCFF360SWK.tabix.bed.gz.dvc | 106.0 B | 53f08349ea1352d3a5e4be85d4891ff9 |
| ENCFF360SWK.tabix.bed.gz.tbi | 401.1 KB | af8caf0991522ebeb9514c55c5a0e3ae |
| ENCFF360SWK.tabix.bed.gz.tbi.dvc | 110.0 B | a480d9920504536de14476977e138683 |
| genomic_resource.yaml | 3.76 KB | 37251a645703c9ff3b9941521b20996f |
| genomic_resource_original.yaml | 3.66 KB | e05e95890a7555e226b312e6147c3e2e |
| statistics/ |