DNase-seq_ENCSR301RCD
DNase-seq ENCSR301RCD [biosample_summary="Homo sapiens renal pelvis tissue male embryo (127 days)"]
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| Id: | DNase-seq/ENCSR301RCD |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR301RCD [biosample_summary="Homo sapiens renal pelvis tissue male embryo (127 days)"] |
| Description: |
status: released biological_replicates: Rep 1 summary: male embryo (127 days) output_type: peaks audit_warning: Alignment file {ENCFF646GPT|/files/ENCFF646GPT/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 30585813 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 {ENCFF646GPT|/files/ENCFF646GPT/} 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/}) |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| DNase-seq_ENCSR301RCD | float |
DNase-seq_ENCSR301RCD |
DNase-seq ENCSR301RCD [biosample_summary="Homo sapiens renal pelvis tissue male embryo (127 days)"]
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[0.263, 21.1] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF073RBO.bed.gz | 356.79 KB | 31529a07fb623c70953f226b6e96183f |
| ENCFF073RBO.bed.gz.dvc | 100.0 B | 48ffdf4cfcfddb45fbc66a54534831f7 |
| ENCFF073RBO.tabix.bed.gz | 318.96 KB | c1414318bd29d1b4e43812bf667077a4 |
| ENCFF073RBO.tabix.bed.gz.dvc | 106.0 B | 776529974808a9a158aad0d635fb54bf |
| ENCFF073RBO.tabix.bed.gz.tbi | 208.63 KB | 08a053b9e060849d380595a5849d4229 |
| ENCFF073RBO.tabix.bed.gz.tbi.dvc | 110.0 B | f9a1b97f0dd4266ef225b5620deb6989 |
| genomic_resource.yaml | 2.66 KB | 2f5de72da1f9f9a622f7dee2da367397 |
| genomic_resource_original.yaml | 2.56 KB | b1cf85c66abae740f4105a9e8603d0cf |
| statistics/ |