I'm working with RNA_Seq data from non-model organisms after differential gene expression analysis I find out their are lot of genes starting with prefix "LOC" and further searched in web I found out that these are genes which don't have any orthologs. I further performed downstream analysis I unable to convert LOC's into ENTREZID's/ENSEMBL ID's using clusterprofiler(bitr function). How do I proceed further for downstream analysis something line GO/KEGG analysis. Should I ignore them completely ? I had total of 7 samples after differential gene expression analysis they found to be 4501 for each sample.
If I search these ID's in NCBI I getting the gene information.