DNase-seq_ENCSR000EPQ
DNase-seq ENCSR000EPQ [biosample_summary="Homo sapiens keratinocyte female"]
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| Id: | DNase-seq/ENCSR000EPQ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR000EPQ [biosample_summary="Homo sapiens keratinocyte female"] |
| Description: |
status: released biological_replicates: Rep 1 summary: female output_type: peaks audit_warning: Replicate 2_1 has no significant footprints detected. audit_warning: Alignment file {ENCFF996YAL|/files/ENCFF996YAL/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 23796928 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: Alignment file {ENCFF142ZLU|/files/ENCFF142ZLU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 32152119 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 {ENCFF996YAL|/files/ENCFF996YAL/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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/}) 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 {ENCFF142ZLU|/files/ENCFF142ZLU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.28. 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_ENCSR000EPQ | float |
DNase-seq_ENCSR000EPQ |
DNase-seq ENCSR000EPQ [biosample_summary="Homo sapiens keratinocyte female"]
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[0.254, 20.1] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF011WVC.bed.gz | 538.96 KB | 80124af6f8365e2453a3e3895ec90e28 |
| ENCFF011WVC.bed.gz.dvc | 100.0 B | c0205fe50dd2f3d63f583269417515d0 |
| ENCFF011WVC.tabix.bed.gz | 478.02 KB | 036784f06b9c9ddee3d918dbb78cbd31 |
| ENCFF011WVC.tabix.bed.gz.dvc | 106.0 B | 1941ed838d20563fc7c753189e1fe3b1 |
| ENCFF011WVC.tabix.bed.gz.tbi | 293.65 KB | 4672414900b215bad6fe9fbc225e474f |
| ENCFF011WVC.tabix.bed.gz.tbi.dvc | 110.0 B | ae08702a96f5217087d5410afcadd4be |
| genomic_resource.yaml | 4.08 KB | 5dd83cea1107c085014867f8eb682197 |
| genomic_resource_original.yaml | 4.0 KB | a92ab494cdedb3d5770ae7f2182284c7 |
| statistics/ |