DNase-seq_ENCSR000EQE
DNase-seq ENCSR000EQE [biosample_summary="Homo sapiens T-helper 1 cell male adult (33 years)"]
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| Id: | DNase-seq/ENCSR000EQE |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR000EQE [biosample_summary="Homo sapiens T-helper 1 cell male adult (33 years)"] |
| Description: |
status: released biological_replicates: Rep 1 summary: male adult (33 years) output_type: peaks audit_internal_action: Archived analysis {ENCAN957AEM|/analyses/ENCAN957AEM/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_not_compliant: Replicate concordance in DNase-seq experiments is measured by calculating the Pearson correlation between signal quantification of the replicates. ENCODE processed signal files {ENCFF795TGF|/files/ENCFF795TGF/}, {ENCFF730AXF|/files/ENCFF730AXF/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a Pearson correlation of 0.85. According to ENCODE standards, in an isogenic assay a Pearson correlation value > 0.9 is recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq/} ) audit_warning: Alignment file {ENCFF329FPF|/files/ENCFF329FPF/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 20520963 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 {ENCFF437UDA|/files/ENCFF437UDA/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 20373691 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 {ENCFF765IRM|/files/ENCFF765IRM/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.25. 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/}) 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 {ENCFF437UDA|/files/ENCFF437UDA/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) 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/}) |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| DNase-seq_ENCSR000EQE | float |
DNase-seq_ENCSR000EQE |
DNase-seq ENCSR000EQE [biosample_summary="Homo sapiens T-helper 1 cell male adult (33 years)"]
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[4, 1.06e+03] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF742OKP.bed.gz | 617.46 KB | a1bf55f544d4166c8d48dd4659cac21e |
| ENCFF742OKP.bed.gz.dvc | 100.0 B | 4325c760c6060681f6235d896b5de23b |
| ENCFF742OKP.tabix.bed.gz | 532.93 KB | 2a8b922d34e88b45757a835d895f5ac3 |
| ENCFF742OKP.tabix.bed.gz.dvc | 106.0 B | b20cf8b3205613f71bbc0dc3c53f7ca0 |
| ENCFF742OKP.tabix.bed.gz.tbi | 291.48 KB | e1e21b3e655cdba2e326f1ab736eeb09 |
| ENCFF742OKP.tabix.bed.gz.tbi.dvc | 110.0 B | 33da4bbcba9289e6214ec09a29fd3d2f |
| genomic_resource.yaml | 4.78 KB | fd59046cc1a5322c464fb9a2672352e9 |
| genomic_resource_original.yaml | 4.69 KB | 21626f803e564bdd430f322f4cfa83be |
| statistics/ |