Resource
| Id | DNase-seq/ENCSR000EPU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EPU [biosample_summary="Homo sapiens epithelial cell of prostate"] |
| Description |
status: released biological_replicates: Rep 2 summary: output_type: peaks audit_internal_action: Archived analysis {ENCAN574TXJ|/analyses/ENCAN574TXJ/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF222FBW|/files/ENCFF222FBW/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 35026810 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 {ENCFF026UXE|/files/ENCFF026UXE/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 35632996 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 {ENCFF879BNX|/files/ENCFF879BNX/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 34705945 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 {ENCFF983FBQ|/files/ENCFF983FBQ/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 35293367 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 {ENCFF879BNX|/files/ENCFF879BNX/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) 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/}) 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 {ENCFF983FBQ|/files/ENCFF983FBQ/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR000EPU | float |
DNase-seq_ENCSR000EPU |
DNase-seq ENCSR000EPU [biosample_summary="Homo sapiens epithelial cell of prostate"]
|
 |
[4, 6.83e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 15706727 | 0.49% | 104561 |
| chr1 | 1431000 | 0.57% | 9521 |
| chr2 | 1307400 | 0.54% | 8699 |
| chr3 | 1096477 | 0.55% | 7296 |
| chr4 | 909450 | 0.48% | 6053 |
| chr5 | 921000 | 0.51% | 6136 |
| chr6 | 991457 | 0.58% | 6601 |
| chr7 | 798000 | 0.50% | 5315 |
| chr8 | 751800 | 0.52% | 5007 |
| chr9 | 661800 | 0.48% | 4404 |
| chr10 | 733144 | 0.55% | 4879 |
| chr11 | 770700 | 0.57% | 5136 |
| chr12 | 792846 | 0.59% | 5279 |
| chr13 | 441600 | 0.39% | 2936 |
| chr14 | 491850 | 0.46% | 3274 |
| chr15 | 500850 | 0.49% | 3335 |
| chr16 | 438367 | 0.49% | 2917 |
| chr17 | 561000 | 0.67% | 3732 |
| chr18 | 393391 | 0.49% | 2621 |
| chr19 | 426150 | 0.73% | 2841 |
| chr20 | 399750 | 0.62% | 2661 |
| chr21 | 187941 | 0.40% | 1252 |
| chr22 | 229904 | 0.45% | 1531 |
| chrX | 431400 | 0.28% | 2873 |
| chrY | 39450 | 0.07% | 262 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 104561 | 94 | 450 | 150.22 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF632UNR.bed.gz | 1009.16 KB | 8f2c896968e16b4992d4b1ea9fc03df5 |
| ENCFF632UNR.tabix.bed.gz | 869.37 KB | 5481629f7b187d8849298d438a6a9077 |
| ENCFF632UNR.tabix.bed.gz.tbi | 515.24 KB | 70ff634ab2214bbd6fabe4b6dc99c417 |
| genomic_resource.yaml | 5.46 KB | 54d2eae819d9f584107d3343a67079af |
| statistics/ |