Hi DESeq fans and Michael love who designed. Learning pretty fast and getting output files. But need to put in the files, the gene symbol and have tried the library(biomaRt) approach , runs but does not put GS into my data. Seems biomart can handle the ensemble ids if functional (seems maybe link between ensemble and biomaRt is not functioning, but biomart is ok) but not sure how to convert mstrg rows so I have gene symbol. I found a nice converter for ensemble id working outside of R that will work for ensemble ids but does not know what to do with these mstrg gene ids from the stringtie output.
Also, in attributes, since mouse, tried mgi_id and mgi_symbol, entrezgene and others, all run but no data, just an NA in that column ,say for entrezgene as an example.
Thanks for the help. steve
This is not a DESeq2 software question so I’ve removed the tag. There are annotation resources on Bioconductor that can help. Take a look at the annotation workflows for example.
You're more likely to get a helpful response if you include a small example of what you're trying to do e.g. if biomaRt didn't achieve the result you want show this with some code. That way others here can try to run your example to help diagnose the issue or suggest a solution.