Question about scRNA-seq Galaxy tutorial


Thank you for making this community of help for Galaxy. I appreciate it. I am a Galaxy instance admin for my institute and creating a single-cell RNA-seq analysis workflow for the instance. I am using this tutorial - Hands-on: Pre-processing of Single-Cell RNA Data / Single Cell. I had a doubt crop up when going through the tutorial. The dataset that the tutorial is using is paired fastq files from Zenodo provided by the authors. It mentions “Paired-end dataset collection” under “Library type” under “Hands-on: Barcode extraction”. However, for the next step which is alignment using STAR, it says “Single-end” (Hands-on: Pre-processing of Single-Cell RNA Data / Single Cell). Does this mean that the first fastq file has only UMI and the second has actual reads? Are all single-cell data similar? I apologize if this is a naive question. I just want to make sure that I am setting up the workflow properly and being clear in the tutorial that I create for my institute. Thank you for all the help!


Hi @Priyanka_Bhandary

Yes, your assumptions are correct.

Review the first few tutorials in the Single-Cell category of tutorials to learn how to interpret the files, and to double check that your specific data is organized the same way.

This is probably the best place to start given your questions → Hands-on: Understanding Barcodes / Single Cell

Please let us know if that actually answers your questions :slight_smile:

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Thank you so much

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