Finding new transcripts in single-cell RNA-Seq datasets

[miaeyaho]

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,

Miae

[jennaj]

Hi @miaeyaho

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

scRNAseq Galaxy workflow

Hello Galaxy folks, I have been using galaxy for a while to analyse RNAseq and I think it’s incredible. Now I was wondering if there would be any workflow to work with single cell RNAseq data from FASTQ files. I have been trying to follow-up these tutorials But so far I couldn’t finish it so I was wondering if any of you know about a complete workflow. I liked this one from the EMBL-EBI https://www.youtube.com/watch?v=1w4sA-qyO3g but they use data from GXA as the source, so the preproce…

Thanks!