DNase-seq_ENCSR941SMM
DNase-seq ENCSR941SMM [biosample_summary="Homo sapiens stomach tissue embryo (101 days)"]
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| Id: | DNase-seq/ENCSR941SMM |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR941SMM [biosample_summary="Homo sapiens stomach tissue embryo (101 days)"] |
| Description: |
status: released biological_replicates: Rep 1 summary: embryo (101 days) output_type: peaks audit_internal_action: Archived analysis {ENCAN462CKY|/analyses/ENCAN462CKY/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF429HHU|/files/ENCFF429HHU/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 35121807 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 {ENCFF348UDP|/files/ENCFF348UDP/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 34842959 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 {ENCFF348UDP|/files/ENCFF348UDP/} 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_ENCSR941SMM | float |
DNase-seq_ENCSR941SMM |
DNase-seq ENCSR941SMM [biosample_summary="Homo sapiens stomach tissue embryo (101 days)"]
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[4, 1.36e+03] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF785AIA.bed.gz | 617.75 KB | bdb97057a2b9b1a3c21a45f43498b386 |
| ENCFF785AIA.bed.gz.dvc | 100.0 B | 96fd71a4f3fb2b4c7e54c2aba65bb0d4 |
| ENCFF785AIA.tabix.bed.gz | 529.01 KB | 653146bddfeb6a0a691f2a12ac1e42a4 |
| ENCFF785AIA.tabix.bed.gz.dvc | 106.0 B | 6032ed7d683d20b316d9f1944c20ee5e |
| ENCFF785AIA.tabix.bed.gz.tbi | 320.68 KB | d2a75fa705d9f5de4619a095c3e5400d |
| ENCFF785AIA.tabix.bed.gz.tbi.dvc | 110.0 B | 7570460663040d77f19b868b9eddd0a9 |
| genomic_resource.yaml | 3.36 KB | 7175b3172625a947e038105654c621ea |
| genomic_resource_original.yaml | 3.27 KB | a2023a8cc2076d7b7e0d0c5b49d48b0e |
| statistics/ |