I'm using the Blast2GO / OmicsBox interface to annotate my RNA-seq data. I've ran all of the analyses (Blast, InterPro, GOmapping, Annotation) and now want to analyze the KEGG pathways. But when I run KEGG analysis through Blast2GO, it's not returning a lot of KEGG pathways even for genes that I thought were well-annotated (glutathione S-transferase, ATP-binding cassette, some cytochrome p450s, etc) and would have well-defined KEGG pathways. Is there something I'm missing in my analysis? Or is there another platform where I can run KEGG analysis?
Thanks in advance.