...
Table of Contents | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
|
The NF-OSI is piloting a new initiative to uniformly process genomic and transcriptomic data that is shared on the NF Data Portal. All studies funded by the Neurofibromatosis Therapeutic Acceleration Program uploaded within the duration 2018 to 2023 are included in the scope of this initiative. The processing of high dimensional genomic and transcriptomic data will be done using standardized data processing pipelines.
...
Eligibility criteria for data files to be staged for processing
...
Table of Contents | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Data files must be annotated with the following details:
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 recommendedRequired 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 recommendedRequired 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 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
...