DNase-seq_ENCSR000ENX
DNase-seq ENCSR000ENX [biosample_summary="Homo sapiens dermis blood vessel endothelial cell female adult"]
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| Id: | DNase-seq/ENCSR000ENX |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR000ENX [biosample_summary="Homo sapiens dermis blood vessel endothelial cell female adult"] |
| Description: |
status: released biological_replicates: Rep 2 summary: female adult output_type: peaks audit_error: 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 {ENCFF807STB|/files/ENCFF807STB/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.19. 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: Alignment file {ENCFF409JXE|/files/ENCFF409JXE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 24707781 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 {ENCFF807STB|/files/ENCFF807STB/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 33364789 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 {ENCFF409JXE|/files/ENCFF409JXE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.37. 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_ENCSR000ENX | float |
DNase-seq_ENCSR000ENX |
DNase-seq ENCSR000ENX [biosample_summary="Homo sapiens dermis blood vessel endothelial cell female adult"]
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[0.271, 14.8] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF609ZYN.bed.gz | 361.95 KB | 82190d8647b48470c37b5a06fae58f55 |
| ENCFF609ZYN.bed.gz.dvc | 100.0 B | d78a97458caac1b5811bff69ed80c68f |
| ENCFF609ZYN.tabix.bed.gz | 323.22 KB | 6c424ba27144a97f417165edb221c273 |
| ENCFF609ZYN.tabix.bed.gz.dvc | 106.0 B | 809a301fa3f25ecf596516dbd862e9ca |
| ENCFF609ZYN.tabix.bed.gz.tbi | 214.26 KB | b9f489f05f51b79ce9adc1b2df104ae8 |
| ENCFF609ZYN.tabix.bed.gz.tbi.dvc | 110.0 B | 3cc2691056cdab67573772fb65ee5790 |
| genomic_resource.yaml | 4.1 KB | 5b8adf2dfea49cd560d518aa738124ac |
| genomic_resource_original.yaml | 3.99 KB | 02efd192ed69674cdf1e5040f3d5c45d |
| statistics/ |