I have RNA data from 10 samples of Cannabis plant. I am planning to do the following analyses with these samples
-) De novo Assembly (ex: Trinity, Velvet, SOAPdenovo, etc. Which is recommended for plants?)
-) Variant calling ( does GATK support plant variant calling?
-) Functional annotation like COG, GO, KEGG, swissprot, NR database (ex: BLAST2GO tool, any other recommendation)
-) Differential gene expression (DESEQ2 or EDGER or LIMMA, which one is recommended for plant dataset?)