Entering edit mode
14 months ago
ankit.yadav
•
0
Hey there! I'm really curious about creating Seurat inputs without using Cell Ranger, as we've got our own sequencer and have done the sequencing in-house. Has anyone else tried this approach or can offer some guidance on how to go about it? Any help or insights would be greatly appreciated!
Seurat accepts any count matrix from any source basically. There is lots of preprocessing software for single-cell data, be it CellRanger itself, STARsolo, alevin-fry, kallisto-bustools and probably others as well. Sure, this is possible without CellRanger, and choice of tool does not depend on whether you or others do the sequencing. It only depends on what single-cell technology you use. CellRanger is exclusively for 10x Chromium, the others are a lot more generic and open-source.
As your question indicates that you're relatively new to this, please try to ask a precise technical question. Reading the manuals of mentioned tools is on you.