Hello,
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!
Priyanka
