Hi everyone,
i've been following through the hisat2-strintie-deseq2 pipeline for my samples using the msu7 rice genome as the reference (http://rice.uga.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/). Now that the alignment process is done, the gene_id looks like this:
LOC_Os06g17030 LOC_Os11g01380 LOC_Os05g38810 LOC_Os01g43480
After Deseq2 analysis i have a list of DEGs and based on previous papers that i referred to i ran GO enrichment with agriGO. Now, i would like to perform kegg enrichment & pathway analysis but im so confused as to how to do it. Im assuming i'll need to convert my MSU gene_id to entrez id to run KEGG analysis. So, i attempted to convert all my gene_ids from MSU to RAP format with RAP-DB (https://rapdb.dna.affrc.go.jp/tools/converter/run) and then used DAVID (https://david.ncifcrf.gov/conversion2.jsp) to convert them to entrez_id. But im losing so much data in between the conversion process. I seem to be really confused on how to move forward from here. Any advice on how i can proceed with my analysis especially for KEGG enrichment?
Thank you
