ATAC-seq_ENCSR304ZDQ
ATAC-seq ENCSR304ZDQ [biosample_summary="Homo sapiens GM18873"]
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| Id: | ATAC-seq/ENCSR304ZDQ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
ATAC-seq ENCSR304ZDQ [biosample_summary="Homo sapiens GM18873"] |
| Description: |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN746KGZ|/analyses/ENCAN746KGZ/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} 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. {ENCFF719MMH|/files/ENCFF719MMH/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has a FRiP score of 0.16. 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 {ENCFF589DFL|/files/ENCFF589DFL/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.814406. 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 {ENCFF589DFL|/files/ENCFF589DFL/} 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) {ENCFF719MMH|/files/ENCFF719MMH/} (overlap peaks) and {ENCFF557BSF|/files/ENCFF557BSF/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 121078 and 69897 peaks. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| ATAC-seq_ENCSR304ZDQ | float |
ATAC-seq_ENCSR304ZDQ |
ATAC-seq ENCSR304ZDQ [biosample_summary="Homo sapiens GM18873"]
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[1.47, 29.7] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF719MMH.bed.gz | 2.87 MB | 48db02ace0d477881b15d02b1a601eea |
| ENCFF719MMH.bed.gz.dvc | 101.0 B | 8bce8600b36ca0ba55233249f137e726 |
| ENCFF719MMH.tabix.bed.gz | 870.68 KB | 74f6ece63bddac74695dc017b2c3c561 |
| ENCFF719MMH.tabix.bed.gz.dvc | 106.0 B | 20b672a57b0b0013394a126e31e30085 |
| ENCFF719MMH.tabix.bed.gz.tbi | 376.26 KB | f537d8f37eca434905a252aa8af8c7ae |
| ENCFF719MMH.tabix.bed.gz.tbi.dvc | 110.0 B | 2a632e27485d6d58e26d58b17c8d4e5f |
| genomic_resource.yaml | 3.47 KB | 58ce2ef4defb9491db52e54c24a8e637 |
| genomic_resource_original.yaml | 3.4 KB | 2b2f02129c76bf75f8647d88fb4ce4d6 |
| statistics/ |