Hi I have output from stringtie and making count files with prepDE.py. I then analyze with DESeq2 and have a list of DE genes. I have in this file both ensemble id and mstrg names for the genes and transcript files. I want to convert those mstrg and ensemble names to gene symbols for downstream analysis. How do I do that. Thanks steve

There are other packages in Bioconductor that can help with adding other labels. See this section of our workflow:

https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#annotating-and-exporting-results