DEGS analysis with DESeq2?

Question

[mathavanbioinfo]

Hello all, I am working in DEG analysis using DESeq2, I followed the protocol given in StringTie, the results file has very few genes ( mapped with AnnotationDbi,org.Hs.eg.db), and the genes start with MSTRG abundantly present. Is there any way to map MSTRG id gene ids or how to deal with that those ids.

[ATpoint]

Unless you really need stringtie in order to assemble a transcriptome just save yourself the trouble with this tool and use anything else. This workflow gives a much more simplistic while not at all less accurate suggestion on how to perform DGE from scratch:

https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

[MatthewP]

Can you show us your StringTie command?