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Datatypes eligible for processing
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title | Whole Exome Sequencing |
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A technique that focuses on sequencing only the exons, which are the coding regions of the genome, of an individual's DNA. WES is used to identify genetic variations in these regions that may be associated with certain diseases or traits. |
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title | Single cell RNA sequencing |
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A technique that involves sequencing the transcriptome of individual cells. This technique provides information on the gene expression levels of each cell and is commonly used to study cell heterogeneity and identify rare cell populations. |
Required annotations for data files to be staged for processing
For each of the following assays, data files must be annotated with the terms listed below.
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Bulk and Single Cell RNA Sequencing
| Annotation term | Additional Details |
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1 | | |
2 | individualID | Individual IDs are necessary to create the sample sheets. |
3 | specimenID | specimen IDs are necessary to interpret the analysis. |
4 | Assay | Choose between Bulk RNA Seq or Single Cell RNA Seq. |
5 | Species | The corresponding genome requires knowledge of the species. |
6 | libraryPreparationMethod | This refers to the name of the library preparation, such as KAPA Hyper PCR 3. |
7 | | |
8 | readPair | Specify whether the read pair is 1 or 2. |
9 | specimenPreparationMethod | Minimize RNA degradation with methods such as flash freezing or RNALater. FFPE is not recommended. |
10 | tumorType | If the tissue is normal, indicate "not applicable." Otherwise, specify the tumor type. |
11 | isStranded* | This answer should be either "yes" or "no." |
12 | readPairOrientation* | Indicate the read pair orientation, such as forward or reverse. |
* optional but recommended
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Whole Genome Sequencing
| Annotation term | Additional Details |
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1 | | |
2 | individualID | Individual IDs are necessary to create the sample sheets. |
3 | specimenID | specimen IDs are necessary to interpret the analysis. |
4 | Assay | Choose between Bulk RNA Seq or Single Cell RNA Seq. |
5 | Species | The corresponding genome requires knowledge of the species. |
6 | libraryPreparationMethod | This refers to the name of the library preparation, such as KAPA Hyper PCR 3. |
7 | | |
8 | readPair | Specify whether the read pair is 1 or 2. |
9 | specimenPreparationMethod | Minimize RNA degradation with methods such as flash freezing or RNALater. FFPE is not recommended. |
10 | tumorType | |
11 | isStranded* | This answer should be either "yes" or "no." |
12 | readPairOrientation* | Indicate the read pair orientation, such as forward or reverse. |
* optional but recommended
...
Whole Exome Sequencing
| Annotation term | Additional Details |
---|
1 | | |
---|
2 | individualID | Individual IDs are necessary to create the sample sheets. |
---|
3 | specimenID | specimen IDs are necessary to interpret the analysis. |
---|
4 | Assay | Choose between Bulk RNA Seq or Single Cell RNA Seq. |
---|
5 | Species | The corresponding genome requires knowledge of the species. |
---|
6 | libraryPreparationMethod | This refers to the name of the library preparation, such as KAPA Hyper PCR 3. |
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7 | | |
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8 | readPair | Specify whether the read pair is 1 or 2. |
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9 | specimenPreparationMethod | Minimize RNA degradation with methods such as flash freezing or RNALater. FFPE is not recommended. |
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10 | tumorType | |
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11 | isStranded* | This answer should be either "yes" or "no." |
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12 | readPairOrientation* | Indicate the read pair orientation, such as forward or reverse. |
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* optional but recommended
Note |
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Additional requirement: The BED file associated with the library preparation method for each WES dataset is required to be uploaded and available to the NF-OSI Sage Team for the dataset to be eligible for processing. |
Assay-specific workflow availability
The table below shows the availability of processing workflows for different data files generated through various ‘omics assays.
Assay | Germline SNV | Somatic SNV | Copy Number Variation (CNV) | Structural variants (SV) | Microsatellite Instability (MSI) | Raw counts |
WES | ✅ | ✅ | ✖️ | ✖️ | ✅ | |
WGS | ✅ | ✅ | ✅ | ✅ | ✅ | |
Bulk RNAseq | | | | | | ✅ |
Single Cell RNAseq | | | | | | ✅ |
✅ The workflow is available for this datatype
✖️ The workflow is available for this data type, but the NF-OSI will not provide this processing. This decision follows from the recommendation of scientists and engineers at Sage who have worked with these data modalities and have noted various problems in interpretation of processed data from these workflows during downstream analysis.
The workflow is not applicable for this data type.