I am a novice in all things bioinformatics and I'm facing some questions with my De novo transcriptome assembly.
I have assembled and assessed the quality of the transcriptome so far. How do I find out a set of specific genes related to a particular function in the organism? My end goal is to develop SSR markers and design primers for the genes related to a certain pathway in the organism. Any suggestions as to how I may proceed? Are there any established pipelines to be followed?
P.S. I mined SSR markers for the assembled transcriptome in whole, but again, I need to filter SSR markers for specific genes only.