DNase-seq_ENCSR888UPQ
DNase-seq ENCSR888UPQ [biosample_summary="Homo sapiens thymus tissue male embryo (108 days)"]
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| Id: | DNase-seq/ENCSR888UPQ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR888UPQ [biosample_summary="Homo sapiens thymus tissue male embryo (108 days)"] |
| Description: |
status: released biological_replicates: Rep 1 summary: male embryo (108 days) output_type: peaks audit_warning: Alignment file {ENCFF945FMY|/files/ENCFF945FMY/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 27188033 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 {ENCFF945FMY|/files/ENCFF945FMY/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.27. 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_ENCSR888UPQ | float |
DNase-seq_ENCSR888UPQ |
DNase-seq ENCSR888UPQ [biosample_summary="Homo sapiens thymus tissue male embryo (108 days)"]
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[0.295, 16.2] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF339ARK.bed.gz | 363.56 KB | 40065574d7c0655bc5b8d5f048635ed5 |
| ENCFF339ARK.bed.gz.dvc | 100.0 B | 8c50b7a7fd97001e8b3d0fc03c4d93b0 |
| ENCFF339ARK.tabix.bed.gz | 325.83 KB | ffcba9d0381bed8401e2421fbfc12668 |
| ENCFF339ARK.tabix.bed.gz.dvc | 106.0 B | 389fab89cef67ee4638f9d355b0c2264 |
| ENCFF339ARK.tabix.bed.gz.tbi | 212.16 KB | eba5e2643153921727d8d6d8af1db624 |
| ENCFF339ARK.tabix.bed.gz.tbi.dvc | 110.0 B | 0cd7157a76a4a8cb41784949d1535062 |
| genomic_resource.yaml | 2.64 KB | 4a285a3813d7c0af59bdfc524d9045db |
| genomic_resource_original.yaml | 2.55 KB | fccf6a66c2972d1c5d1c3adc33b52001 |
| statistics/ |