How do I choose the right tutorial for my platform?¶
There is a platform tutorial for each of these platforms: 10x Xenium, Vizgen MERSCOPE, CosMx SMI, 10x Visium HD, Stereo-seq, Seq-Scope, and Pixel-seq, plus a Generic tutorial for any other platform's transcript table. Each starts from a small dataset, shows the single run_together command, and then walks through the individual commands.
For your own data, see the platform's page under Platforms: it lists the exact files run_together looks for and example commands. Built-in profiles exist for 10x Xenium, 10x Visium HD, CosMx SMI, MERSCOPE (MERFISH), Illumina, Stereo-seq, and Seq-Scope, plus a generic profile for anything else.
If your platform is not listed above, see: