I'm working on Rice rnaseq data. Kallisto was used for the pseudo-alignment. I have to questions:
1- I have 6 conditions 2 replicates each (12 samples in total), how can I do multiple condition testing to get the differential expressed genes? I tried sleuth and deseq2 but I couldn't do all the conditions at once. is there a way to do that?
2- The gene names are in that format : OS11T* , I can't do the further gene annotation for the genes? Any idea how to do it?
Thanks in advance.