DNase-seq_ENCSR000EOQ
DNase-seq ENCSR000EOQ [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn"]
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| Id: | DNase-seq/ENCSR000EOQ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR000EOQ [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn"] |
| Description: |
status: released biological_replicates: Rep 1 summary: newborn output_type: peaks audit_warning: Alignment file {ENCFF400NFM|/files/ENCFF400NFM/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 31477814 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 {ENCFF400NFM|/files/ENCFF400NFM/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.30. 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/}) 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 {ENCFF374GNN|/files/ENCFF374GNN/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.38. 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_ENCSR000EOQ | float |
DNase-seq_ENCSR000EOQ |
DNase-seq ENCSR000EOQ [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn"]
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[0.0196, 22.5] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF080VVT.bed.gz | 1.9 MB | e68283fe7c73626e0459f97ec4c27fa8 |
| ENCFF080VVT.bed.gz.dvc | 101.0 B | 99ab8db71a0b550f892d21ea5b503756 |
| ENCFF080VVT.tabix.bed.gz | 1.76 MB | 0630fd9cb4fd5f1e854c4478da2aee68 |
| ENCFF080VVT.tabix.bed.gz.dvc | 107.0 B | beeb5a2873f644322a94d49b3f1164d9 |
| ENCFF080VVT.tabix.bed.gz.tbi | 532.59 KB | 87d399b602aca76637aaf155268a0baf |
| ENCFF080VVT.tabix.bed.gz.tbi.dvc | 110.0 B | c5dda152ade88e71c1829c4eb66debe9 |
| genomic_resource.yaml | 3.62 KB | 37a1b5daf1cac6a2a7cefd00422d3065 |
| genomic_resource_original.yaml | 3.51 KB | ebd6ab2924b27d9251f6adffd5bf2e24 |
| statistics/ |