DNase-seq_ENCSR475VQD
DNase-seq ENCSR475VQD [biosample_summary="Homo sapiens brain tissue male embryo (72 days) and male embryo (76 days)"]
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| Id: | DNase-seq/ENCSR475VQD |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR475VQD [biosample_summary="Homo sapiens brain tissue male embryo (72 days) and male embryo (76 days)"] |
| Description: |
status: released biological_replicates: Rep 1 summary: male embryo (72 days) male embryo (76 days) output_type: peaks audit_warning: Alignment file {ENCFF878NAE|/files/ENCFF878NAE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 42397848 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 {ENCFF878NAE|/files/ENCFF878NAE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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_ENCSR475VQD | float |
DNase-seq_ENCSR475VQD |
DNase-seq ENCSR475VQD [biosample_summary="Homo sapiens brain tissue male embryo (72 days) and male embryo (76 days)"]
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[0.0266, 42.9] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF224LZZ.bed.gz | 2.64 MB | 80e8cfdb09f17636c7b4e77572207e82 |
| ENCFF224LZZ.bed.gz.dvc | 101.0 B | 961cbd5ed0ff8abe72dbb7385c53803d |
| ENCFF224LZZ.tabix.bed.gz | 2.42 MB | 72f4e39fae16ae391ba9276252a05892 |
| ENCFF224LZZ.tabix.bed.gz.dvc | 107.0 B | e5dc3e04be521c0e5dc7fe3368c20c97 |
| ENCFF224LZZ.tabix.bed.gz.tbi | 768.23 KB | 6f493dbe6f7ea1663a36b6d6307f781f |
| ENCFF224LZZ.tabix.bed.gz.tbi.dvc | 110.0 B | 35306a38e0c8effa060cd4fea66dcc23 |
| genomic_resource.yaml | 2.76 KB | 0fc708b75a6561125d94753450afdb5e |
| genomic_resource_original.yaml | 2.64 KB | 4dfa380579af4a5a43d6ed5b95a6c116 |
| statistics/ |