Hi, I am working on rice. I have a question here that which software is better for gene ontology and KEGG pathway analysis? I have already used "AgriGo" online tool for analysis, but it is giving error in bar (graphical) representation.
You can use MapMan. I found that it has more gene annotations for rice than other tools. It has to be locally installed together with the specific annotation file for the species. More details here: https://mapman.gabipd.org/
For 'Oryza sativa japonica (Japanese rice) (RefSeq)' from KEGG: osa
./prepare_database -db=KEGG -org=osa ./geneSCF -m=normal -i=INPUTgene.list -t=sym -db=KEGG -o=/ExistingOUTPUTfolder/ -org=osa --plot=no --background=#num_genes
For 'Oryza sativa japonica (Japanese rice) (RAPDB)' from KEGG: dosa
./prepare_database -db=KEGG -org=dosa ./geneSCF -m=normal -i=INPUTgene.list -t=sym -db=KEGG -o=/ExistingOUTPUTfolder/ -org=dosa --plot=no --background=#num_genes
Check other KEGG organism/species codes here to use in GeneSCF.