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Data Types in the scope of processing:
Whole exome sequencing dataExome Sequencing
Whole genome sequencing dataGenome Sequencing
Bulk RNA sequencing dataSequencing
Single cell RNA sequencing data
Eligibility criteria for data files to be staged for processing:
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Raw data files present in the study must have file format annotated as “fastq” or “bam” or “cram”
Required annotations for 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. |
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Data files must originate from samples that were “flash frozen”. Data from FFPE samples are not eligible for processing due to possible degradation of genomic samples due to the preservation process.
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Data files must have the required minimal annotations according to the NF-OSI data model (as suggested in the NF Data Curator App). These annotations include among others:
individualID
specimenID
assay
libraryPreparationMethod
Platform
isStranded
readPairOrientation
readPair
specimenPreparationMethod
isCellLine
isXenograft
species
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Only raw data files uploaded to Synapse projects are eligible to be staged for processing at this time.
Ineligibility criteria for specific processing methods:
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WES files are not eligible for structural variant calling or copy number variant calling
| 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. |
* optional but recommended
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Required annotations for Whole Genome 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. 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. |
* optional but recommended
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Required annotations for Whole Exome 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. 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 |
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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. |
* optional but recommended
Availability of processing workflows:
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