Resource
| Id | DNase-seq/ENCSR000EMT |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EMT [biosample_summary="Homo sapiens GM12878"] |
| Description |
status: released biological_replicates: Rep 2 summary: output_type: peaks audit_warning: Alignment file {ENCFF020WZB|/files/ENCFF020WZB/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 22289382 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 {ENCFF729UYK|/files/ENCFF729UYK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 38560136 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 {ENCFF020WZB|/files/ENCFF020WZB/} 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/}) 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 {ENCFF729UYK|/files/ENCFF729UYK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.36. 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_ENCSR000EMT | float |
DNase-seq_ENCSR000EMT |
DNase-seq ENCSR000EMT [biosample_summary="Homo sapiens GM12878"]
|
 |
[0.21, 31.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10232455 | 0.32% | 50475 |
| chr1 | 965281 | 0.39% | 4751 |
| chr2 | 788512 | 0.33% | 3900 |
| chr3 | 648609 | 0.33% | 3207 |
| chr4 | 486120 | 0.26% | 2417 |
| chr5 | 569953 | 0.31% | 2786 |
| chr6 | 668483 | 0.39% | 3281 |
| chr7 | 492185 | 0.31% | 2482 |
| chr8 | 454829 | 0.31% | 2246 |
| chr9 | 398873 | 0.29% | 2004 |
| chr10 | 482763 | 0.36% | 2414 |
| chr11 | 495172 | 0.37% | 2415 |
| chr12 | 545887 | 0.41% | 2642 |
| chr13 | 240056 | 0.21% | 1197 |
| chr14 | 334523 | 0.31% | 1649 |
| chr15 | 336233 | 0.33% | 1712 |
| chr16 | 346834 | 0.38% | 1702 |
| chr17 | 458213 | 0.55% | 2233 |
| chr18 | 211520 | 0.26% | 1063 |
| chr19 | 438582 | 0.75% | 2071 |
| chr20 | 262525 | 0.41% | 1297 |
| chr21 | 114702 | 0.25% | 556 |
| chr22 | 199111 | 0.39% | 988 |
| chrX | 293052 | 0.19% | 1459 |
| chrY | 437 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 50475 | 2 | 820 | 202.72 | 200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF759OLD.bed.gz | 541.94 KB | 72e37cbf02fc8958a73a3b8fe20c8cf6 |
| ENCFF759OLD.tabix.bed.gz | 485.07 KB | dfbbce8e426628d4d8e9b1c7ffcc1828 |
| ENCFF759OLD.tabix.bed.gz.tbi | 276.46 KB | a15ce17ae53f37e2a63a7d7d9c5a7ca7 |
| genomic_resource.yaml | 4.2 KB | d9371ffbae77fad9ed7c190fd4add067 |
| statistics/ |