DNase-seq_ENCSR000EMT
DNase-seq ENCSR000EMT [biosample_summary="Homo sapiens GM12878"]
×
| 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: |
|
| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| DNase-seq_ENCSR000EMT | float |
DNase-seq_ENCSR000EMT |
DNase-seq ENCSR000EMT [biosample_summary="Homo sapiens GM12878"]
|
|
[0.21, 31.4] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF759OLD.bed.gz | 541.94 KB | 72e37cbf02fc8958a73a3b8fe20c8cf6 |
| ENCFF759OLD.bed.gz.dvc | 100.0 B | 1f046e72f54ab115cf3a650e25b6cd77 |
| ENCFF759OLD.tabix.bed.gz | 485.07 KB | dfbbce8e426628d4d8e9b1c7ffcc1828 |
| ENCFF759OLD.tabix.bed.gz.dvc | 106.0 B | 88016d3a30d36e072c115040e22948f0 |
| ENCFF759OLD.tabix.bed.gz.tbi | 276.46 KB | a15ce17ae53f37e2a63a7d7d9c5a7ca7 |
| ENCFF759OLD.tabix.bed.gz.tbi.dvc | 110.0 B | 00a03c3ab5eb81ba5ad6e2a05f72d984 |
| genomic_resource.yaml | 4.2 KB | d9371ffbae77fad9ed7c190fd4add067 |
| genomic_resource_original.yaml | 4.13 KB | e623bdb91744c5279238154a56906016 |
| statistics/ |