I have been following the pathway HISAT2->StringTie->StringTie merge->Gff compare->FeatureCounts->Deseq2 for my RNA-seq analysis, as described in here: https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/de-novo/tutorial.html
Everything worked nicely, but at the level of differential expression, DEseq2 is giving this error:
Error in parse(text = x, keep.source = FALSE) :
:1:4: unexpected symbol
1: ~ 1X2X3XvsX4X5X6
Calls: as.formula … formula -> formula.character -> formula -> eval -> parse
Any idea what could have caused it and how to fix it?