DNase-seq_ENCSR133SPH
DNase-seq ENCSR133SPH [biosample_summary="Homo sapiens large intestine tissue female embryo (120 days)"]
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| Id: | DNase-seq/ENCSR133SPH |
| Type: | position_score |
| Version: | 0 |
| Summary: |
DNase-seq ENCSR133SPH [biosample_summary="Homo sapiens large intestine tissue female embryo (120 days)"] |
| Description: |
status: released biological_replicates: Rep 1 summary: female embryo (120 days) output_type: peaks audit_internal_action: Archived analysis {ENCAN964FJP|/analyses/ENCAN964FJP/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF521WIQ|/files/ENCFF521WIQ/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 29710972 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 {ENCFF541OSD|/files/ENCFF541OSD/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 29464215 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 {ENCFF541OSD|/files/ENCFF541OSD/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.37. 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: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| DNase-seq_ENCSR133SPH | float |
DNase-seq_ENCSR133SPH |
DNase-seq ENCSR133SPH [biosample_summary="Homo sapiens large intestine tissue female embryo (120 days)"]
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[4, 1.43e+03] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF472DJP.bed.gz | 851.83 KB | 7605214c600c2846fa7ac0d2bf5f4660 |
| ENCFF472DJP.bed.gz.dvc | 100.0 B | cd8a4d4515d7f836e4caf79660ec86f8 |
| ENCFF472DJP.tabix.bed.gz | 730.77 KB | bd1e6922458252d5e32e269a31a0559b |
| ENCFF472DJP.tabix.bed.gz.dvc | 106.0 B | 2870c1bbdea899832c4478a50ad9b58c |
| ENCFF472DJP.tabix.bed.gz.tbi | 429.51 KB | 789a3f1d1c223ea548f753f46b4414bb |
| ENCFF472DJP.tabix.bed.gz.tbi.dvc | 110.0 B | b0fcee97838cbfb330f0700b0e4f17f9 |
| genomic_resource.yaml | 3.41 KB | 500a2699ecbd841265c1b155f37fa742 |
| genomic_resource_original.yaml | 3.31 KB | 7bab8e3757b42268abf0026e17b06498 |
| statistics/ |