Hi, how can the single nuclei rna seq data be pre-processed in galaxy? What changes should be made to the sc rna seq tutorial? I know that both exons and introns should be mapped, but other than that, what changes should be made on STARSolo?
Hello! Other than that, I’d say not much! As long as it doesn’t reject intronic reads, you should be fine. Filtering becomes a lot trickier because there’s usually a lot more background and a lot less RNA per cell, so you’ll have to be really careful of what cut-offs you use in the pre-processing stages. @mtekman Are there any STARSolo changes that need to be made here? I used Alevin, and even then, I couldn’t necessarily tell you if intronic reads would break it or not!
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Hard to say! The only way to know is to try 
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