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Why the cell numbers in ArchR project differed from the results from cellranger-atac #2318
Description
Hello，
I am using ArchR to analyse my single cell ATAC-seq data, but I noticed a difference in the cell numbers in the result of cellranger-atac between ArchR project. In my ArchR project, I got 20693 cells, while in the results of cellranger, it is 19256 cells.
I am unsure why this difference exists and would greatly appreciate your insights on:
Potential reasons for the cell count mismatch between ArchR and cellranger-atac
Recommended steps to validate and reconcile these cell numbers (e.g., filtering criteria, data processing steps)
Thank you very much for your time and assistance.
Activity
immanuelazn commentedon Dec 25, 2025
Hi @CampingOnSeabed! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
If you are getting an error, it is likely due to something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help.
Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for.
If your post does not contain a reproducible example, it is unlikely to receive a response.
In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information:
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
2. Did you post your log file? If not, add it now.
3. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.