I have transcriptome data of an inhouse sequenced bacterial genome. I made the database for my bacteria using makeOrgPackageFromNCBI command.
How can I use this database for KEGG AND Go analysis (ORA or GSEA). All commands use either KEGG organism database for such an analysis. I tried with that command (KEGGrich command) but it indicated that "Gene ids did not match" as output.
If I want to use the above method, where I use the closest strain to my species from the KEGG database. I had a set of gene ID (eg: R30_hybrid_002367) for which I have extracted KO, Go ids using eggnog tool. can I map these Ko ids as Term2gene, how can I extract term2name database for this?
If KEGG database of a closet species (with term2gene and term2name) for analysis and I have identified the KO ids of my filtered DEGs using eggnog, but for some gene such as sRNAs or hypothetical protein, I do not have the Ko ids. I will miss those gene ids from my analysis?
Please help me solve this issue.