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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.

The datatypes in the scope of processing include:

• Whole Exome Sequencing

• Whole Genome Sequencing

• Bulk RNA Sequencing

• Single cell RNA sequencing

The uniformly processed data will be shared on the NF Data Portal and will also be used to support the use of data from the NF Data Portal in other data analysis/exploration platforms. 

The processing of high dimensional genomic and transcriptomic data will be done using standardized data processing pipelines.

Thanks to the generosity of the NF-OSI funders, a subset of the NF Data Portal data is currently eligible for reprocessing as part of this initiative. If you have a dataset that you have shared on the NF Data Portal and would like to utilize the NF-OSI Processing pipelines, please reach out to us at nf-osi@sagebionetworks.org. We would be happy to assist you in a case-by-case basis.Read the checklist below to learn more about which data are currently eligible for reprocessing.  

Studies in the current scope of this initiative:

All studies funded by the Neurofibromatosis Therapeutic Acceleration Program that uploaded data within the duration 2018 to 2023.

Data Types in the scope of processing:

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Whole Exome Sequencing

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Whole Genome Sequencing

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Bulk RNA Sequencing

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Eligibility criteria for data files to be staged for processing:

Required annotations for RNA Sequencing

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* optional but recommended

Availability of processing workflows:

The table below shows the availability of processing workflows for different data files generated through various ‘omics assays. 

✅ means the workflow is Available for the data files 

❌ means the workflow is available for these kind of data files 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. 

NA means the workflow is not applicable for these data files

^{✅ 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.} 

^{NA The workflow is not applicable for this data type.}