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Required Annotations for Genomic Processing

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
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
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
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.