De-novo transcriptome

Question

[bala]

I am conducting transcriptome analysis on a parasitic plant for which no whole genome is available. I would appreciate assistance in suggesting steps for analysis after Trinity assembly, including differential expression analysis, identification of coding sequences (CDSs), KEGG pathway analysis, and other relevant analyses.

Thank you for your suggestions

[Ram]

steps steps for analysis after Trinity assembly, including differential expression analysis, identification of coding sequences (CDSs)

You're already listing different analysis paths, why don't you pick one of them and ask for help when you run into actual problems? Also, this post does not have a finite number of "correct" responses, so it should not be a Question-type post. It is better suited as a Forum discussion. Please edit your post and reclassify it.