Resource
| Id | DNase-seq/ENCSR000EQE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EQE [biosample_summary="Homo sapiens T-helper 1 cell male adult (33 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (33 years) output_type: peaks audit_internal_action: Archived analysis {ENCAN957AEM|/analyses/ENCAN957AEM/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_not_compliant: Replicate concordance in DNase-seq experiments is measured by calculating the Pearson correlation between signal quantification of the replicates. ENCODE processed signal files {ENCFF795TGF|/files/ENCFF795TGF/}, {ENCFF730AXF|/files/ENCFF730AXF/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a Pearson correlation of 0.85. According to ENCODE standards, in an isogenic assay a Pearson correlation value > 0.9 is recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq/} ) audit_warning: Alignment file {ENCFF329FPF|/files/ENCFF329FPF/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 20520963 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 {ENCFF437UDA|/files/ENCFF437UDA/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 20373691 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 {ENCFF765IRM|/files/ENCFF765IRM/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.25. 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 {ENCFF437UDA|/files/ENCFF437UDA/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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_ENCSR000EQE | float |
DNase-seq_ENCSR000EQE |
DNase-seq ENCSR000EQE [biosample_summary="Homo sapiens T-helper 1 cell male adult (33 years)"]
|
 |
[4, 1.06e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9527475 | 0.30% | 63335 |
| chr1 | 937560 | 0.38% | 6226 |
| chr2 | 755452 | 0.31% | 5025 |
| chr3 | 607307 | 0.31% | 4039 |
| chr4 | 416620 | 0.22% | 2766 |
| chr5 | 493146 | 0.27% | 3278 |
| chr6 | 612422 | 0.36% | 4069 |
| chr7 | 445729 | 0.28% | 2966 |
| chr8 | 391193 | 0.27% | 2601 |
| chr9 | 391500 | 0.28% | 2603 |
| chr10 | 449701 | 0.34% | 2993 |
| chr11 | 453680 | 0.34% | 3011 |
| chr12 | 494287 | 0.37% | 3289 |
| chr13 | 251239 | 0.22% | 1668 |
| chr14 | 323111 | 0.30% | 2143 |
| chr15 | 311114 | 0.31% | 2068 |
| chr16 | 324933 | 0.36% | 2158 |
| chr17 | 465415 | 0.56% | 3095 |
| chr18 | 174269 | 0.22% | 1162 |
| chr19 | 398109 | 0.68% | 2648 |
| chr20 | 229441 | 0.36% | 1527 |
| chr21 | 105737 | 0.23% | 703 |
| chr22 | 179460 | 0.35% | 1196 |
| chrX | 292800 | 0.19% | 1947 |
| chrY | 23250 | 0.04% | 154 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 63335 | 23 | 450 | 150.43 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF742OKP.bed.gz | 617.46 KB | a1bf55f544d4166c8d48dd4659cac21e |
| ENCFF742OKP.tabix.bed.gz | 532.93 KB | 2a8b922d34e88b45757a835d895f5ac3 |
| ENCFF742OKP.tabix.bed.gz.tbi | 291.48 KB | e1e21b3e655cdba2e326f1ab736eeb09 |
| genomic_resource.yaml | 4.78 KB | fd59046cc1a5322c464fb9a2672352e9 |
| statistics/ |