DNase-seq_ENCSR682PKY
DNase-seq ENCSR682PKY [biosample_summary="Homo sapiens thymus tissue female embryo"]
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| Id: | DNase-seq/ENCSR682PKY |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR682PKY [biosample_summary="Homo sapiens thymus tissue female embryo"] |
| Description: |
status: released biological_replicates: Rep 1 summary: female embryo output_type: peaks audit_internal_action: Archived analysis {ENCAN519MPX|/analyses/ENCAN519MPX/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF810FRM|/files/ENCFF810FRM/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 32705402 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/}) audit_warning: Alignment file {ENCFF139RJL|/files/ENCFF139RJL/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 32461431 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/}) 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 {ENCFF139RJL|/files/ENCFF139RJL/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.40. 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/}) |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| DNase-seq_ENCSR682PKY | float |
DNase-seq_ENCSR682PKY |
DNase-seq ENCSR682PKY [biosample_summary="Homo sapiens thymus tissue female embryo"]
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[3, 1.36e+03] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF186QHO.bed.gz | 699.61 KB | 681e22a3474d3fa7412091dd3bad1a4c |
| ENCFF186QHO.bed.gz.dvc | 100.0 B | 232cc1ac972e5e533be93b1115dc0258 |
| ENCFF186QHO.tabix.bed.gz | 602.27 KB | bbc0f3b390c9cc88584a096ddc8c98fc |
| ENCFF186QHO.tabix.bed.gz.dvc | 106.0 B | e6f588a510aabfbb820e1d4c32643c04 |
| ENCFF186QHO.tabix.bed.gz.tbi | 350.94 KB | 51f542f3d76064392eb5a19577fe8660 |
| ENCFF186QHO.tabix.bed.gz.tbi.dvc | 110.0 B | 09f98300dc73657e452685df828a551f |
| genomic_resource.yaml | 3.33 KB | 5437b66b8534cf39d418871367cd6de4 |
| genomic_resource_original.yaml | 3.24 KB | 0d02613682bcbee383df5ff57fe5df98 |
| statistics/ |