Hello everyone. Before I head to my questions, I would like to brief on my current project. I'm working on the transcriptomic analysis on the parasitic plant, Rafflesia sp. My interest is to treasure the uniqueness in the parasite-host interaction which will be between Rafflesia sp. and it's host Tetrastigma sp. I have collected some of the samples from the bud stage of the Rafflesia sp. and used for the RNA extraction.
The samples that I wish to study are the Disk sample from Rafflesia sp. and the haustorium tissue which is considered as the multi-tissue samples (contains tissues from Rafflesia sp. as well as the Tetrastigma sp.). I have received the raw data of both samples and wish to conduct bioinformatics analysis using these samples. As for now I have no replicates for both samples.
So the question on the analysis would be, what kind of pipeline shall i use to further the analysis after I have assembly the raw data? Will there be any problems in conducting the analysis without having a replicate? Currently, I have assemble both samples data and I'm stucked to where will be my next pipeline destination. Please give me suggestion on how to move forward with this data since it involved two different RNA tissues.
Thank in advance for your responses.
If the study is mainly just to identify the genes involved, with least focus on the DEG, would it better? I would say my primary goal will be to identify the function of certain genes during the interaction between these two organisms.