Resource
| Id | DNase-seq/ENCSR000ELP |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000ELP [biosample_summary="Homo sapiens RWPE1"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: peaks audit_error: Alignment file {ENCFF497SLL|/files/ENCFF497SLL/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 652848 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_internal_action: Archived analysis {ENCAN103OKD|/analyses/ENCAN103OKD/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} 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 {ENCFF497SLL|/files/ENCFF497SLL/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.35. 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 |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR000ELP | float |
DNase-seq_ENCSR000ELP |
DNase-seq ENCSR000ELP [biosample_summary="Homo sapiens RWPE1"]
|
 |
[6, 89] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 171900 | 0.01% | 1145 |
| chr1 | 18450 | 0.01% | 123 |
| chr2 | 11100 | <0.01% | 74 |
| chr3 | 7500 | <0.01% | 50 |
| chr4 | 5100 | <0.01% | 33 |
| chr5 | 15900 | 0.01% | 106 |
| chr6 | 7950 | <0.01% | 53 |
| chr7 | 7800 | <0.01% | 52 |
| chr8 | 5250 | <0.01% | 35 |
| chr9 | 10500 | 0.01% | 70 |
| chr10 | 9900 | 0.01% | 66 |
| chr11 | 11250 | 0.01% | 75 |
| chr12 | 8550 | 0.01% | 57 |
| chr13 | 2100 | <0.01% | 14 |
| chr14 | 4050 | <0.01% | 27 |
| chr15 | 6900 | 0.01% | 46 |
| chr16 | 5550 | 0.01% | 37 |
| chr17 | 10950 | 0.01% | 73 |
| chr18 | 1650 | <0.01% | 11 |
| chr19 | 9450 | 0.02% | 63 |
| chr20 | 7800 | 0.01% | 52 |
| chr21 | 1050 | <0.01% | 7 |
| chr22 | 1500 | <0.01% | 10 |
| chrX | 1650 | <0.01% | 11 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 1145 | 150 | 300 | 150.13 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF065JGY.bed.gz | 12.18 KB | 9115afdbcb09852518552d3655f61242 |
| ENCFF065JGY.tabix.bed.gz | 10.35 KB | 782e9ce7d49475e600d19793a792e84a |
| ENCFF065JGY.tabix.bed.gz.tbi | 16.91 KB | 81bff7726a11612aeca8b6561f0ae418 |
| genomic_resource.yaml | 2.7 KB | 9faa2f6527e81543b37c8013015125de |
| statistics/ |