I noticed that my count and annotate files do not have the same number of lines (rows). How can I fix this?
what is the origin of your samples and what type annotation file you are using?
I sorted it out. It appears that if I chose Ensemble in the “outputs columns” of annotateMyIDs tools in addition to ENTREZID I get extra lines int he annotate files compared to Count files.
So to fix this, I re-ran the tool and de-selected Ensemble from the “outputs columns”