ATAC-seq_ENCSR086OGH
ATAC-seq ENCSR086OGH [biosample_summary="Homo sapiens sigmoid colon tissue male adult (54 years)"]
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| Id: | ATAC-seq/ENCSR086OGH |
| Type: | position_score |
| Version: | 0 |
| Summary: |
ATAC-seq ENCSR086OGH [biosample_summary="Homo sapiens sigmoid colon 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 {ENCAN657AGV|/analyses/ENCAN657AGV/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN657AGV|/analyses/ENCAN657AGV/} has in progress subobject document {35df17fc-b139-4395-9a89-85afc3648f31|/documents/35df17fc-b139-4395-9a89-85afc3648f31/} 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. {ENCFF270JNZ|/files/ENCFF270JNZ/} 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 {ENCFF182ZGK|/files/ENCFF182ZGK/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.874348. 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 {ENCFF182ZGK|/files/ENCFF182ZGK/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.88. 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) {ENCFF270JNZ|/files/ENCFF270JNZ/} (overlap peaks) and {ENCFF697MUB|/files/ENCFF697MUB/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 110999 and 60532 peaks. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| ATAC-seq_ENCSR086OGH | float |
ATAC-seq_ENCSR086OGH |
ATAC-seq ENCSR086OGH [biosample_summary="Homo sapiens sigmoid colon tissue male adult (54 years)"]
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[1.5, 28.6] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF270JNZ.bed.gz | 2.63 MB | 527acde68e0be423b391318d071243cb |
| ENCFF270JNZ.bed.gz.dvc | 101.0 B | 17bf620d11d12a10f4271f6bf69bf537 |
| ENCFF270JNZ.tabix.bed.gz | 751.53 KB | 370567116ff1f7c7a7e13b993638594c |
| ENCFF270JNZ.tabix.bed.gz.dvc | 106.0 B | 7c798fe3fb7fbd6e3843c3f000c2c520 |
| ENCFF270JNZ.tabix.bed.gz.tbi | 351.83 KB | a3a56568436112a5b0e4ee80c7f09c7f |
| ENCFF270JNZ.tabix.bed.gz.tbi.dvc | 110.0 B | 438a614eebdeafc1de8582fffc833f9f |
| genomic_resource.yaml | 3.74 KB | 108f0f69e09775530d2b8f0564af4cba |
| genomic_resource_original.yaml | 3.64 KB | 37bd65d09daef0eac00baf1b5986c6af |
| statistics/ |