Required Annotations for Genomic Processing
- Jineta Banerjee
- Christina Parry
Owned by Jineta Banerjee
For each of the following assays, data files must be annotated with the terms listed below to be staged for processing.
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. |
* optional but recommended
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 | Whole Genome Sequencing |
| 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
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 | Whole Exome Sequencing |
| 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
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.