Finding new transcripts in single-cell RNA-Seq datasets

Hi everyone,

I am looking for a workflow to find new transcripts in scRNA-Seq datasets. Do you know what galaxy tools could be used for this analysis?

I had a experience to analyze transcripts in bulk RNA-Seq data using HISAT2 - StringTie pipeline.

I am wondering if these tools can be used for scRNA data, or if I can use another tool inside the Galaxy for this task. If StringTie can be used for scRNA, I would appreciate if if you could tell me how to use it.

It would be great if someone knew how to proceed with this analysis.

Stay healthy.
Many thanks,


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Hi @miaeyaho

Please see this prior Q&A. There is a Galaxy GTN tutorial/workflow that covers this analysis.