DNase-seq_ENCSR000ENM
DNase-seq ENCSR000ENM [biosample_summary="Homo sapiens HCT116"]
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| Id: | DNase-seq/ENCSR000ENM |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR000ENM [biosample_summary="Homo sapiens HCT116"] |
| Description: |
status: released biological_replicates: Rep 2 summary: output_type: peaks audit_warning: Alignment file {ENCFF969VWM|/files/ENCFF969VWM/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 26087726 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 {ENCFF304MDQ|/files/ENCFF304MDQ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 30888113 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 {ENCFF304MDQ|/files/ENCFF304MDQ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) 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-encode4/}) |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| DNase-seq_ENCSR000ENM | float |
DNase-seq_ENCSR000ENM |
DNase-seq ENCSR000ENM [biosample_summary="Homo sapiens HCT116"]
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[0.228, 48.2] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF240LRP.bed.gz | 715.99 KB | 7ac7c1d3717ec5ead65b83847be4c8b0 |
| ENCFF240LRP.bed.gz.dvc | 100.0 B | 7be010375321d2563aa191a73428c197 |
| ENCFF240LRP.tabix.bed.gz | 644.26 KB | 80d7af703bcf28d4fef9543bbc5a01cb |
| ENCFF240LRP.tabix.bed.gz.dvc | 106.0 B | 228208c64ce38feddbf43fea8f23fe9b |
| ENCFF240LRP.tabix.bed.gz.tbi | 353.32 KB | a545671897cde07b04ae178816ea2df4 |
| ENCFF240LRP.tabix.bed.gz.tbi.dvc | 110.0 B | ebf4464aceafad58ed48cf0e6b0236ec |
| genomic_resource.yaml | 3.2 KB | 6c2237715a7cfc2a86eae3d31c65c7a7 |
| genomic_resource_original.yaml | 3.13 KB | e2d64f8593a495eeaa8c217b1adb9a41 |
| statistics/ |