I've got 3 rna seq datasets Im trying to integrate and there are ~1000genes with different aliases across sets (when I integrate them these genes do not merge appropriately as the Seurat package assumes these different aliases are in fact different genes)
Is there any easy way to go about homogenizing all of these? I've tried the online converters but that has not worked very well? Logically it seems easy to convert all of these to ensembl or entrez IDs and then convert back to gene IDs, but since these are sc-rna-seq datasets there is a variety of "gene names" which are for alignment/normalization that get lost during the conversion process since they aren't actually genes (these are of course needed for my downstream analysis). If I have a list of the ~1000 aliases, is there an easy way to search for these aliases in my datasets and replace with a single gene name?