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Analysis of single-cell RNA sequencing data with STARsolo

Here we will describe the pipeline for processing raw single-cell RNA sequencing reads with STARsolo. In addition, we touch on the approach for dealing with technical replicates of the same sample that have undergone separate sequencing runs.

We also cover how to download publicly available scRNAseq data from the SRA database using the SRA Toolkit.

Steps

1. Downloading publicly available scRNAseq data: a guide to downloading data from the NCBI SRA database using the SRA Toolkit.
2. Mapping reads to the genome: use our Nextflow pipeline – nf-mucimmuno/scRNAseq – to run quality control steps (FastQC and TrimGalore!) on raw sequencing reads, followed by mapping to the host genome using STARsolo.

3. Quality control: continue with data pre-processing, using the outputs from STARsolo.