DNase-seq_ENCSR511GQA
DNase-seq ENCSR511GQA [biosample_summary="Homo sapiens stomach tissue female embryo (108 days)"]
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| Id: | DNase-seq/ENCSR511GQA |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR511GQA [biosample_summary="Homo sapiens stomach tissue female embryo (108 days)"] |
| Description: |
status: released biological_replicates: Rep 1 summary: female embryo (108 days) output_type: peaks audit_error: Alignment file {ENCFF222ICK|/files/ENCFF222ICK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 19745618 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 {ENCFF222ICK|/files/ENCFF222ICK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.32. 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_ENCSR511GQA | float |
DNase-seq_ENCSR511GQA |
DNase-seq ENCSR511GQA [biosample_summary="Homo sapiens stomach tissue female embryo (108 days)"]
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[0.407, 20.9] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF066YJZ.bed.gz | 336.31 KB | dabbfd15d7143cbbc40b3d4bea2e20a2 |
| ENCFF066YJZ.bed.gz.dvc | 100.0 B | 00433cd51b9f48983bdd5d5a0e29c65f |
| ENCFF066YJZ.tabix.bed.gz | 296.28 KB | 7c6fa33d40fb159e2c7eaa713cd48b99 |
| ENCFF066YJZ.tabix.bed.gz.dvc | 106.0 B | f84e48f777494816c24d9e5ccfdc684d |
| ENCFF066YJZ.tabix.bed.gz.tbi | 225.11 KB | fe59d2c74fbebfe4b0717e5473f022ae |
| ENCFF066YJZ.tabix.bed.gz.tbi.dvc | 110.0 B | 95c1a504813ce88e6a2bc501010cb62f |
| genomic_resource.yaml | 2.65 KB | 8f8bcc833a45a3b7942649034559a7b5 |
| genomic_resource_original.yaml | 2.55 KB | bb81df0fb0db59141ef4cfafd7630345 |
| statistics/ |