Seurat can not save outputs into rds or Rscript ?

Hi, there

I ran Seurat version 3.1.2 on UseGalaxy, eventhough this toolkit says it can output rds file or R script, but there are no any buttons to save outputs into these datatypes. Is there a way to know how the web interface outputs arguments into the Rscript or rds file?


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With version 3.1.2, the new wrapper for seurat outputs in the style of a customizable r markdown instead. You can choose to just have the R code appear in the output via selection at the bottom of the tool. You can have just the graphs, some hybrid of the code and graphs, or all of both on the output file.


I’m having this issue as well. The Seurat tool still says:

But there is no RDS output. This means none of the other Seurat tools can be used e.g. below:

Without an RDS Object output it’s also difficult to share with colleagues planning to do further analysis.

Which older versions output the RDS Object?

I am using the HumanCellAtlast instance at

Hi there - is there an option to use an older version of Seurat if we’d like to get the RDS file?


I think @astrov is talking about this:


Thanks @David, maybe I cam confused about the outputs - isn’t the RDS file different to the R code?

@carolyn_nielsen we try to not use rds formats, as they tend to be variant formats with contents we can’t read very well. If you want the datasets in that format, you can use output the datasets alongside the code, then run that in RStudio to retrieve the datasets themselves?

I have just submitted a change in the wrapper to remove that text and avoid confusion. Sorry about that.

@astrov Thanks for the reply- I can try that with my collaborator but I had also wanted to use some of the other Seurat tools within Galaxy that require ‘RDS with a Seurat object’ as the input file.

These look like they are designed for 10X data (mine is plate-based SmartSeq, Nextera Libraries), but may be an option to use the ‘Seurat Read10x’ tool with my tabular counts file to out the RDS object? Should that work without a metadata file?

I’m currently getting an error message but looks like might be a server issue rather than with the tool.

It looks as though you might want to use the CreateSeuratObject tool in that case?

Yes agree but that tool requires the Read 10X tool first, right?

You would be correct. I just saw the tool name and assumed, sorry