DNase-seq_ENCSR726YMS
DNase-seq ENCSR726YMS [biosample_summary="Homo sapiens stomach tissue female embryo"]
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| Id: | DNase-seq/ENCSR726YMS |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR726YMS [biosample_summary="Homo sapiens stomach tissue female embryo"] |
| Description: |
status: released biological_replicates: Rep 1 summary: female embryo output_type: peaks audit_internal_action: Archived analysis {ENCAN496DUS|/analyses/ENCAN496DUS/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF958QZF|/files/ENCFF958QZF/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 33599301 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 {ENCFF430FMO|/files/ENCFF430FMO/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 33352159 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 {ENCFF430FMO|/files/ENCFF430FMO/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.39. 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_ENCSR726YMS | float |
DNase-seq_ENCSR726YMS |
DNase-seq ENCSR726YMS [biosample_summary="Homo sapiens stomach tissue female embryo"]
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[4, 1.7e+03] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF716YVE.bed.gz | 821.85 KB | fa26e46e42a63d1d97ba929eb95a6af5 |
| ENCFF716YVE.bed.gz.dvc | 100.0 B | 54610bb1f6de0c24f8c014b7569de4f9 |
| ENCFF716YVE.tabix.bed.gz | 703.79 KB | 1ea9710f1cd472fdb00dab9946009c8d |
| ENCFF716YVE.tabix.bed.gz.dvc | 106.0 B | a03c698e52d49445a55bc1f503aa0e46 |
| ENCFF716YVE.tabix.bed.gz.tbi | 424.96 KB | 82e18d2de96ef0f3ccf85366dce8a7fe |
| ENCFF716YVE.tabix.bed.gz.tbi.dvc | 110.0 B | ac93f3ae7e652cd7223ba54620d9cd6b |
| genomic_resource.yaml | 3.34 KB | 619010e7ac8a66b1d1943051f162c114 |
| genomic_resource_original.yaml | 3.25 KB | c75f8eed06ffcd7629b4913dee8baff3 |
| statistics/ |