ATAC-seq_ENCSR117PYB
ATAC-seq ENCSR117PYB [biosample_summary="Homo sapiens heart left ventricle tissue female adult (51 years)"]
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| Id: | ATAC-seq/ENCSR117PYB |
| Type: | position_score |
| Version: | 0 |
| Summary: |
ATAC-seq ENCSR117PYB [biosample_summary="Homo sapiens heart left ventricle tissue female adult (51 years)"] |
| Description: |
status: released biological_replicates: Rep 1 summary: female adult (51 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN325VHG|/analyses/ENCAN325VHG/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN325VHG|/analyses/ENCAN325VHG/} has in progress subobject document {1fb078ac-8be3-4516-8b6d-5934412c6ecc|/documents/1fb078ac-8be3-4516-8b6d-5934412c6ecc/} 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. {ENCFF544RZR|/files/ENCFF544RZR/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.07. audit_not_compliant: 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) {ENCFF544RZR|/files/ENCFF544RZR/} (overlap peaks) and {ENCFF174HPZ|/files/ENCFF174HPZ/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 84725 and 26918 peaks. audit_warning: Alignment file {ENCFF713UOC|/files/ENCFF713UOC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 24932595 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: 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 {ENCFF713UOC|/files/ENCFF713UOC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.824226. 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 {ENCFF713UOC|/files/ENCFF713UOC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.85. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| ATAC-seq_ENCSR117PYB | float |
ATAC-seq_ENCSR117PYB |
ATAC-seq ENCSR117PYB [biosample_summary="Homo sapiens heart left ventricle tissue female adult (51 years)"]
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[1.62, 19.7] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF544RZR.bed.gz | 1.95 MB | 4c79c86b2843c1f8a9aafc59accb32a5 |
| ENCFF544RZR.bed.gz.dvc | 101.0 B | 6d65f43351e2570aeb50c505bb8f66b7 |
| ENCFF544RZR.tabix.bed.gz | 554.67 KB | 1d60db582cf99bbd97745f292b3c6a9a |
| ENCFF544RZR.tabix.bed.gz.dvc | 106.0 B | 93bf15a7ea9b912b9ca90442be66c82e |
| ENCFF544RZR.tabix.bed.gz.tbi | 288.35 KB | 30883aa3bf9a13fc7619126a115543e8 |
| ENCFF544RZR.tabix.bed.gz.tbi.dvc | 110.0 B | f514022861ac990ba47eb96c000db484 |
| genomic_resource.yaml | 4.14 KB | d81be50224b6a71c39b5474a3040ee2a |
| genomic_resource_original.yaml | 4.03 KB | 580bc96d29b767d1ba4ae5f63713fd3d |
| statistics/ |