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Datatypes eligible for processing
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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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A technique that involves sequencing the entire genome of an individual. This includes both the coding regions and the non-coding regions of DNA. WGS is used to identify genetic variations throughout the entire genome that may be associated with certain diseases or traits. |
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A technique that involves sequencing the transcriptome of a bulk population of cells. This technique provides information on the gene expression levels of all genes in the sample and is commonly used to compare gene expression profiles between different samples or conditions. |
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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. |
Assay-specific workflow availability
The table below shows the availability of processing workflows for different data files generated through various ‘omics assays.
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Assay
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Germline SNV
...
Somatic SNV
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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.
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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 to be staged for processing.
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Bulk and Single Cell RNA Sequencing
Annotation term | Additional Details | |
|---|---|---|
| 1 | fileFormat | Accepted file formats include "fastq", "bam", and "cram". If provided raw data are “bam” or “cram” format, only files that have not undergone any additional filtering (i.e. retains unmapped reads, have not been trimmed, etc) will be eligible for processing. |
| 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 | Platform | This refers to the name of the platform used, for example, illumina. |
| 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. |
...
Annotation term | Additional Details | |
|---|---|---|
| 1 | fileFormat | Accepted file formats include "fastq", "bam", and "cram". If provided raw data are “bam” or “cram” format, only files that have not undergone any additional filtering (i.e. retains unmapped reads, have not been trimmed, etc) will be eligible for processing. |
| 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 | Platform | This refers to the name of the platform used, for example, illumina. |
| 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. NOTE: Files from samples lacking tumor-normal pairs will not be eligible for Somatic variant calls or for microsatellite instability processing. |
| 11 | isStranded* | This answer should be either "yes" or "no." |
| 12 | readPairOrientation* | Indicate the read pair orientation, such as forward or reverse. |
...
Annotation term | Additional Details | |
|---|---|---|
| 1 | fileFormat | Accepted file formats include "fastq", "bam", and "cram". If provided raw data are “bam” or “cram” format, only files that have not undergone any additional filtering (i.e. retains unmapped reads, have not been trimmed, etc) will be eligible for processing. Note: WES files are not eligible for variant calling if BED file is not available |
| 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 | Platform | This refers to the name of the platform used, for example, illumina. |
| 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. NOTE: Files from samples lacking tumor-normal pairs will not be eligible for Somatic variant calls or for microsatellite instability processing. |
| 11 | isStranded* | This answer should be either "yes" or "no." |
| 12 | readPairOrientation* | Indicate the read pair orientation, such as forward or reverse. |
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