ATAC-seq_ENCSR452OSK
ATAC-seq ENCSR452OSK [biosample_summary="Homo sapiens right cardiac atrium tissue male adult (40 years)"]
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| Id: | ATAC-seq/ENCSR452OSK |
| Type: | position_score |
| Version: | 0 |
| Summary: |
ATAC-seq ENCSR452OSK [biosample_summary="Homo sapiens right cardiac atrium tissue male adult (40 years)"] |
| Description: |
status: released biological_replicates: Rep 1 summary: male adult (40 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN237QKD|/analyses/ENCAN237QKD/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN237QKD|/analyses/ENCAN237QKD/} has in progress subobject document {fbb28048-cfb5-40f1-8245-dce1e3c0fa31|/documents/fbb28048-cfb5-40f1-8245-dce1e3c0fa31/} 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. {ENCFF092BBF|/files/ENCFF092BBF/} processed by ATAC-seq ENCODE4 v1.8.0 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) {ENCFF092BBF|/files/ENCFF092BBF/} (overlap peaks) and {ENCFF820DKN|/files/ENCFF820DKN/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline have 70107 and 31063 peaks. audit_warning: Alignment file {ENCFF637IKR|/files/ENCFF637IKR/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline has 24239506 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 {ENCFF637IKR|/files/ENCFF637IKR/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.863969. 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 {ENCFF637IKR|/files/ENCFF637IKR/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.87. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| ATAC-seq_ENCSR452OSK | float |
ATAC-seq_ENCSR452OSK |
ATAC-seq ENCSR452OSK [biosample_summary="Homo sapiens right cardiac atrium tissue male adult (40 years)"]
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[1.41, 18.4] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF092BBF.bed.gz | 1.69 MB | d5db70b6ac32242469ee5007aa96c0a6 |
| ENCFF092BBF.bed.gz.dvc | 101.0 B | 6c58619ccb7b1c0c48f9dc19a2c9421d |
| ENCFF092BBF.tabix.bed.gz | 536.12 KB | 803173215ae0fead592cc6b739f38f83 |
| ENCFF092BBF.tabix.bed.gz.dvc | 106.0 B | 45ccd35a0628eac06a7267d9bcc2d535 |
| ENCFF092BBF.tabix.bed.gz.tbi | 270.06 KB | 027165dd74d36c7cfafee7c12f0be36b |
| ENCFF092BBF.tabix.bed.gz.tbi.dvc | 110.0 B | 3084295777bffaf2bc92a7b4d47416fb |
| genomic_resource.yaml | 4.13 KB | d4aa027692d367c02f4ba1212a8ed38f |
| genomic_resource_original.yaml | 4.02 KB | 8e5376cf5ac1b27553ec8b49f646b0df |
| statistics/ |