DNase-seq_ENCSR422PVL
DNase-seq ENCSR422PVL [biosample_summary="Homo sapiens left kidney tissue female embryo (147 days)"]
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| Id: | DNase-seq/ENCSR422PVL |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR422PVL [biosample_summary="Homo sapiens left kidney tissue female embryo (147 days)"] |
| Description: |
status: released biological_replicates: Rep 1 summary: female embryo (147 days) output_type: peaks audit_internal_action: Archived analysis {ENCAN603XNH|/analyses/ENCAN603XNH/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF159QUF|/files/ENCFF159QUF/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 29684986 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 {ENCFF225BMQ|/files/ENCFF225BMQ/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 29480912 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 {ENCFF225BMQ|/files/ENCFF225BMQ/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.31. 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_ENCSR422PVL | float |
DNase-seq_ENCSR422PVL |
DNase-seq ENCSR422PVL [biosample_summary="Homo sapiens left kidney tissue female embryo (147 days)"]
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[4, 448] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF281XUZ.bed.gz | 567.46 KB | e3a7716c57aaf57bcb3012fc4ced3534 |
| ENCFF281XUZ.bed.gz.dvc | 100.0 B | 91eb37f8e37ec674bea760bd3831387e |
| ENCFF281XUZ.tabix.bed.gz | 484.86 KB | 31cfc2748f0eb523a033bb25db7f8387 |
| ENCFF281XUZ.tabix.bed.gz.dvc | 106.0 B | 97306d199bef2a4addbdadd27e3360d9 |
| ENCFF281XUZ.tabix.bed.gz.tbi | 323.75 KB | 345cbd0ae55cbafc47bcb98bbe0180ef |
| ENCFF281XUZ.tabix.bed.gz.tbi.dvc | 110.0 B | 3a339c5c82566fc5858bf24c8a39d021 |
| genomic_resource.yaml | 3.4 KB | e275f5a2f637f38a4fe1da446b769336 |
| genomic_resource_original.yaml | 3.3 KB | 26708cc9f98c613c86f31aebfa7f12ea |
| statistics/ |