just a tiny suggestion

[opitzl]

Dear Seurat-Dev-Team,
it would be nice if the Read10X function
would support an optional prefix in the CellRanger output data or to read 10X data from GEO without renaming.

[samuel-marsh]

Agree this would be great if implemented.

In meantime as fyi I have written functions to handle such situations (GEO files etc) in my package scCustomize. Read10X_GEO can read in one or more files from same directory with prefixes and if you are reading all files doesn’t require you to specify prefix or files to share prefix (will return list with entries named by prefix).
https://samuel-marsh.github.io/scCustomize/articles/Read_and_Write_Functions.html

Best,
Sam

EDIT. Also apologies if the images are not displaying in vignette linked (they aren’t on mobile for me currently). Will update site next week with new package version release coming.

[samuel-marsh]

Will also add if you want Seurat native solution you can simply use ReadMtx function.

Best,
Sam

[samuel-marsh]

Also actually just remembered ReadMtx was solution added when I sent similar PR while back #4101 . So think that will likely remain supported solution to file prefix/non-standard names.

Best,
Sam

[saketkc]

Hi @opitzl and @samuel-marsh, thanks for the suggestion and discussion. We think ReadMtx is a versatile approach to handle these cases. Thanks for your PR @opitzl - we really appreciate it, but also want to keep the technology specific methods (such as 10X) to do exactly one task. Please use ReadMtx for other use cases.

[samuel-marsh]

Thought as much based on our previous conversations! Thanks again @saketkc!