I’ve been working on a single cell RNA-seq dataset (SMARTSeq, Nextera libraries) with RNASTAR and StringTie, and have visualised the total dataset using Seurat. I’d now like to look at differential expression between two groups but I’m having trouble working out how to do this with the TPM data generated in StringTie. Could someone please advise which DE tools can use this as inputs? Or if there is a way to do DE analyses within the Galaxy version of Seurat? I’ve tried DESeq2 a few times but it hasn’t worked (and the options for input file didn’t sound quite right as either raw counts or TPM from kallisto/salmon/sailfish, rather than StringTie). I haven’t been able to find any tutorials that discuss DE after StringTie specifically. Any advice much appreciated!
Hi @carolyn_nielsen, a detailed explanation of the necessary steps can be found in: