Hi @Jeff
Ok – I see the problem now.
Some of the Bioconductor tools do not understand the “dot” in identifiers. Sort of a gotcha but that is how the tools work everywhere. In short, R is interpreting the dot when it shouldn’t be. I think you can quote it but I haven’t tested that with every tool in this pipeline.
We have a few topics about it if you are curious. The solution can be to remove the .N part of the identifier. This is one example.
The FAQ here has a troubleshooting warning but it is easy to miss!
- FAQ: Extended Help for Differential Expression Analysis Tools
- Sometimes these tools do not understand
transcript_id.Nandgene_id.Nnotation (where N is a version number). - This notation could be in fasta or tabular inputs.
- Try removing
.Nfrom all inputs, and check for the accidential creation of new duplicates!
- Sometimes these tools do not understand
This trips up people using the tools directly, too!
But I’m glad you were able to get this working! You might be able to get the other annotation sources working too. 