Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

General question on batches and Azimuth #140

Open
gsudre opened this issue Mar 20, 2023 · 0 comments
Open

General question on batches and Azimuth #140

gsudre opened this issue Mar 20, 2023 · 0 comments

Comments

@gsudre
Copy link

gsudre commented Mar 20, 2023

Hi, after reading the traditional Seurat integration vignette and the Azimuth FAQ on different batches, I'm struggling to understand what the workflow should be. Am I wrong that Azimuth does not take into consideration the previous clustering results? For example, say I run the integration tutorial, and none of my clusters seems to be related to technical or biological artifacts. Then, I use Azimuth to classify my cells. Couldn't I just have skipped all post-QC steps and gone straight to running Azimuth for each batch individually, and then just continue the analysis from there (e.g. pseudobulk on Azimuth results for cluster A of each batch, then cluster B, etc)? I think I might be missing something! Thanks :)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant