DNase-seq_ENCSR000ENV
DNase-seq ENCSR000ENV [biosample_summary="Homo sapiens mammary epithelial cell female"]
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| Id: | DNase-seq/ENCSR000ENV |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR000ENV [biosample_summary="Homo sapiens mammary epithelial cell female"] |
| Description: |
status: released biological_replicates: Rep 1 summary: female output_type: peaks audit_warning: Alignment file {ENCFF619RSR|/files/ENCFF619RSR/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 30795569 mapped reads. According to ENCODE standards, conventional DNase-seq profile requires a minimum of 20 million uniquely mapped reads to generate a reliable SPOT (Signal Portion of Tags) score. The recommended value is > 50 million. For deep, foot-printing depth DNase-seq 150-200 million uniquely mapped reads are recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) audit_warning: Alignment file {ENCFF698JTA|/files/ENCFF698JTA/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 23997781 mapped reads. According to ENCODE standards, conventional DNase-seq profile requires a minimum of 20 million uniquely mapped reads to generate a reliable SPOT (Signal Portion of Tags) score. The recommended value is > 50 million. For deep, foot-printing depth DNase-seq 150-200 million uniquely mapped reads are recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) audit_warning: Signal Portion of Tags (SPOT) is a measure of enrichment, analogous to the commonly used fraction of reads in peaks metric. ENCODE processed alignment files {ENCFF619RSR|/files/ENCFF619RSR/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.40. According to ENCODE standards, SPOT1 score of 0.4 or higher is considered a product of high quality data. Any sample with a SPOT1 score <0.3 should be targeted for replacement with a higher quality sample, and a SPOT1 score of 0.25 is considered minimally acceptable SPOT1 score of 0.25 is considered minimally acceptable for rare and hard to find primary tissues. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| DNase-seq_ENCSR000ENV | float |
DNase-seq_ENCSR000ENV |
DNase-seq ENCSR000ENV [biosample_summary="Homo sapiens mammary epithelial cell female"]
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[0.264, 39.7] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF628QME.bed.gz | 746.73 KB | 277779ba44ec6253596a33d581d34d24 |
| ENCFF628QME.bed.gz.dvc | 100.0 B | ca5ab4ddb844a985440736023481f555 |
| ENCFF628QME.tabix.bed.gz | 673.2 KB | 4320a8d98fec7dfa6bb6271917667f5b |
| ENCFF628QME.tabix.bed.gz.dvc | 106.0 B | 9fbe3115e9cac201c4d2f4907bfc17b3 |
| ENCFF628QME.tabix.bed.gz.tbi | 368.11 KB | 34180c73d19c356ba27a5cd806cd5015 |
| ENCFF628QME.tabix.bed.gz.tbi.dvc | 110.0 B | ac932c7f2a930f1c85719034716b3c53 |
| genomic_resource.yaml | 3.21 KB | 6bb550396dee4aecf5e0dc3fb62186fe |
| genomic_resource_original.yaml | 3.12 KB | f4c42dc229dec47270083f648dbeb230 |
| statistics/ |