...

If you have not transferred files to the server already, click Image Removed More details here click here for more details and choose to Transfer files to the server. 

• Select the fastq files in the upload folder used for file transfer (select all sample files at one time; including R1 and R2 for each sample) 
• Click Finish

The prefix used for R1 and R2 fastq files should match. 

...

The fastq files will be imported into the project as a unaligned an Unaligned reads node. 

Pre-processing the unaligned fastq files

...

For more information about Space Ranger click here.

If you have not done so already, a Cell Ranger ARC reference should be created.

Image Added

Annotate Visium image

To run Annotate cells:

...