DNase-seq_ENCSR540PVZ
DNase-seq ENCSR540PVZ [biosample_summary="Homo sapiens right renal pelvis tissue male embryo (120 days)"]
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| Id: | DNase-seq/ENCSR540PVZ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR540PVZ [biosample_summary="Homo sapiens right renal pelvis tissue male embryo (120 days)"] |
| Description: |
status: released biological_replicates: Rep 1 summary: male embryo (120 days) output_type: peaks audit_warning: Replicate 1_3 has no significant footprints detected. audit_warning: Alignment file {ENCFF110OQK|/files/ENCFF110OQK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 26201658 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 {ENCFF110OQK|/files/ENCFF110OQK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.38. 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: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| DNase-seq_ENCSR540PVZ | float |
DNase-seq_ENCSR540PVZ |
DNase-seq ENCSR540PVZ [biosample_summary="Homo sapiens right renal pelvis tissue male embryo (120 days)"]
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[0.268, 17.7] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF046KDM.bed.gz | 474.53 KB | ea9a01bc15f59054405fd3923f00c6a9 |
| ENCFF046KDM.bed.gz.dvc | 100.0 B | 9f4a7a435f516b1060eca19d1109063c |
| ENCFF046KDM.tabix.bed.gz | 423.25 KB | 180b66eec706304c8ef845c7f03e1363 |
| ENCFF046KDM.tabix.bed.gz.dvc | 106.0 B | c58bb4b0bf337d8ce4ad095e6465a9fb |
| ENCFF046KDM.tabix.bed.gz.tbi | 263.37 KB | 5cbe327f6a0a753de6e0bcc57fa5b827 |
| ENCFF046KDM.tabix.bed.gz.tbi.dvc | 110.0 B | d90c0ef2d1d14d3708f2851673a840a8 |
| genomic_resource.yaml | 2.76 KB | f09221a775897215d9f2402bc98e2170 |
| genomic_resource_original.yaml | 2.65 KB | 7f24ded75c72bebb5eb73251d07c5735 |
| statistics/ |