DNase-seq_ENCSR000EKD
DNase-seq ENCSR000EKD [biosample_summary="Homo sapiens HuH-7"]
×
| Id: | DNase-seq/ENCSR000EKD |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR000EKD [biosample_summary="Homo sapiens HuH-7"] |
| Description: |
status: released biological_replicates: Rep 1 summary: output_type: peaks audit_error: Alignment file {ENCFF172VLC|/files/ENCFF172VLC/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 249407 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_error: 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 {ENCFF172VLC|/files/ENCFF172VLC/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.22. 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_internal_action: Archived analysis {ENCAN803FVU|/analyses/ENCAN803FVU/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} |
| Labels: |
|
| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| DNase-seq_ENCSR000EKD | float |
DNase-seq_ENCSR000EKD |
DNase-seq ENCSR000EKD [biosample_summary="Homo sapiens HuH-7"]
|
|
[7, 52] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF220TWO.bed.gz | 1.08 KB | 57e4b8833477128a2b6f270b07c6ac66 |
| ENCFF220TWO.bed.gz.dvc | 98.0 B | 673a8ca739e06ebd7b009f798d63246d |
| ENCFF220TWO.tabix.bed.gz | 917.0 B | e43df58f3b68463c5679847c686e1f35 |
| ENCFF220TWO.tabix.bed.gz.dvc | 103.0 B | 0b813871ab0d18e9307c1b3a079cab89 |
| ENCFF220TWO.tabix.bed.gz.tbi | 3.96 KB | 9362b6d804f3fcfe10f394f5243da5a9 |
| ENCFF220TWO.tabix.bed.gz.tbi.dvc | 108.0 B | e8e4b7f4c8fc1030f59f14ac0e6cc187 |
| genomic_resource.yaml | 2.7 KB | c370c806af078c1e0fb083673c5be80f |
| genomic_resource_original.yaml | 2.63 KB | 11ef220b83cd62265357a17638c48afe |
| statistics/ |