Resource
| Id | DNase-seq/ENCSR000EPY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EPY [biosample_summary="Homo sapiens SK-N-MC"] |
| Description |
status: released biological_replicates: Rep 2 summary: output_type: peaks audit_warning: Alignment file {ENCFF813AZG|/files/ENCFF813AZG/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 24053790 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 {ENCFF306JAZ|/files/ENCFF306JAZ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 26905626 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 {ENCFF813AZG|/files/ENCFF813AZG/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.33. 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 {ENCFF306JAZ|/files/ENCFF306JAZ/} 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 |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR000EPY | float |
DNase-seq_ENCSR000EPY |
DNase-seq ENCSR000EPY [biosample_summary="Homo sapiens SK-N-MC"]
|
 |
[0.224, 25.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8761399 | 0.27% | 49257 |
| chr1 | 780461 | 0.31% | 4414 |
| chr2 | 713867 | 0.29% | 4028 |
| chr3 | 615027 | 0.31% | 3417 |
| chr4 | 531414 | 0.28% | 2994 |
| chr5 | 507401 | 0.28% | 2871 |
| chr6 | 663170 | 0.39% | 3669 |
| chr7 | 465446 | 0.29% | 2646 |
| chr8 | 699405 | 0.48% | 3750 |
| chr9 | 345327 | 0.25% | 1949 |
| chr10 | 225609 | 0.17% | 1336 |
| chr11 | 375295 | 0.28% | 2139 |
| chr12 | 462822 | 0.35% | 2625 |
| chr13 | 300205 | 0.26% | 1633 |
| chr14 | 293076 | 0.27% | 1665 |
| chr15 | 235692 | 0.23% | 1331 |
| chr16 | 174352 | 0.19% | 993 |
| chr17 | 253723 | 0.30% | 1453 |
| chr18 | 192089 | 0.24% | 1097 |
| chr19 | 281564 | 0.48% | 1548 |
| chr20 | 201195 | 0.31% | 1132 |
| chr21 | 99387 | 0.21% | 569 |
| chr22 | 103611 | 0.20% | 600 |
| chrX | 240819 | 0.15% | 1395 |
| chrY | 442 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 49257 | 1 | 680 | 177.87 | 178 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF054KLI.bed.gz | 517.0 KB | e14af2841e06f2c4f56bad1fb7cc8d6b |
| ENCFF054KLI.tabix.bed.gz | 459.49 KB | 9650243aad1f824f6ca357566dc87064 |
| ENCFF054KLI.tabix.bed.gz.tbi | 299.74 KB | 9769396055803db935e2f43e43d48103 |
| genomic_resource.yaml | 4.34 KB | f092b87289a9e81a53620e3360a87299 |
| statistics/ |