ATAC-seq_ENCSR955JSO
ATAC-seq ENCSR955JSO [biosample_summary="Homo sapiens breast epithelium tissue male adult (54 years)"]
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| Id: | ATAC-seq/ENCSR955JSO |
| Type: | position_score |
| Version: | 0 |
| Summary: |
ATAC-seq ENCSR955JSO [biosample_summary="Homo sapiens breast epithelium 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 {ENCAN362BBC|/analyses/ENCAN362BBC/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN362BBC|/analyses/ENCAN362BBC/} has in progress subobject document {72e5ee36-e11a-475d-a13a-8bda096d5636|/documents/72e5ee36-e11a-475d-a13a-8bda096d5636/} 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. {ENCFF934JPB|/files/ENCFF934JPB/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.12. 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 {ENCFF344HVC|/files/ENCFF344HVC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.865547. 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 {ENCFF344HVC|/files/ENCFF344HVC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.87. 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) {ENCFF934JPB|/files/ENCFF934JPB/} (overlap peaks) and {ENCFF738IZU|/files/ENCFF738IZU/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 121178 and 62135 peaks. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| ATAC-seq_ENCSR955JSO | float |
ATAC-seq_ENCSR955JSO |
ATAC-seq ENCSR955JSO [biosample_summary="Homo sapiens breast epithelium tissue male adult (54 years)"]
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[1.6, 32.4] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF934JPB.bed.gz | 2.88 MB | 3e196ae9513491b5bf997b8a202cc869 |
| ENCFF934JPB.bed.gz.dvc | 101.0 B | 64bbdfcf1fa2c98bb771236007303f9c |
| ENCFF934JPB.tabix.bed.gz | 848.63 KB | 566cfbe616d66270a9b6eb5122555fb7 |
| ENCFF934JPB.tabix.bed.gz.dvc | 106.0 B | 409f8786e77de5bb83f33e530cfce4e0 |
| ENCFF934JPB.tabix.bed.gz.tbi | 372.49 KB | 10e5dfe17a03c88f44c2bd28a133ae23 |
| ENCFF934JPB.tabix.bed.gz.tbi.dvc | 110.0 B | 7c94fb070994ed8b4872441f316cc3d8 |
| genomic_resource.yaml | 3.75 KB | 34ce88bc2a854514720a18c46427012e |
| genomic_resource_original.yaml | 3.64 KB | 878f14f4bb7844c0bbcef6b8069d5b0f |
| statistics/ |