Question: I ran the single cell multiome ATAC and GEX assay. How can I analyze multiome data on 10x Genomics Cloud Analysis?
Answer: It is possible to analyze samples from the single cell multiome ATAC and GEX assay on 10x cloud. Once you have successfully uploaded the FASTQ files into a project, using either the web uploader or 10x Genomics Cloud CLI tool, you can proceed with the next steps as indicated below.
Note that multiome GEX library and multiome ATAC library need to be analyzed together to be able to get the benefits of the multiome assay such as feature linkage. Thus the FASTQ files need to be simultaneously analyzed in 10x cloud. This is the equivalent of running the Cell Ranger ARC pipeline.
1. Select the appropriate Library of Feature Type from the dropdown menu for both the multiome ATAC and multiome GEX libraries.
2. Select the FASTQ files to be included in the analysis. Once you select FASTQ files belonging to a multiome GEX and multiome ATAC library, this allows you to move to the next steps and the analysis UI. Click on Create New Analysis.
3. After this you can enter the relevant information in the analysis UI and click on Run Analysis.
4. Advanced settings are optionally available and can be set as required.
Now you are set to run your multiome analyses.
Note: 10x Genomics Cloud Analysis is only available in the United States and Canada.