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 gene…

Hi @carolyn_nielsen , a detailed explanation of the necessary steps can be found in: [image] Galaxy Training: De novo transcriptome reconstruction with RNA-Seq Training material for all kinds of transcriptomics analysis. Cheers.

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DE analysis after StringTie

gallardoalba December 2, 2020, 9:10pm 2

Hi @carolyn_nielsen, a detailed explanation of the necessary steps can be found in:

Cheers.

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Issue with StringTie Output File when using DESeq2 option

StringTie error generating gene and transcripts counts files