Please give the workflow for the below question:

You have single cell sequence $($sc seq$)$ data in both $$cell ranger$$ files and fastq. You can start from either.

There are pipelines that do QC$,$ trimming, alignment, etc.

Cell ranger by $10$x also does these steps. These cell rangers generated files $($or the ones from other pipelines$)$ are then used to make UMAPs and DEGs lists, etc.

The things you need to eventually do are

Compare groups to each other, Compare clusters to other clusters. $($and generate gene lists, pathways etc from those comparisons.$)$