rcorces
commented
1 year ago Hi @Goood2001! Thanks for using ArchR! I am currently on vacation and will not be responding to any issues or discussion threads until 5/5.
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.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably 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, how will we 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.
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I'm working with an object which is about 50,000 cells per sample. When I use ArchR addDoubletScores() function to inferring dsciATAC-seq Doublets, there are only a few cells can be detection as doublets and most of cells have low doubleScore. About this issue my solution is using subsetArchRProject() to split my ArrowFiles into 3 or 5 parts and calculate each DoubleScore. Then I can get normal doublets rate. Thus, is there any max level of cell numbers per sample that ArchR can deal with? I guess it's around 10k cells?