I have a medicinal plant that there is a little information on it (it is not sequenced). Do a differential gene expression profile (By RNA-Seq) and a differential metabolic profile (By GC/MS) from stem, root, leaf and fruit help me to get good results on metabolic pathways?
Yes, at least you could have informations about the expressed genes controlling metabolic aspects, enzymes, etc. The GC/MS method will give you metabolic profiling but you must know the pros and cons of this method. The main limitation is that the sample must be easily converted into a gaseous form. If not, you might not be able to record the GC-MS spectrum. The main benefit is that it is a powerful instrument capable of analyzing, separating, and matching all the ingredients of an unknown mixture. The best is to combine both RNA-seq and GC/MS method but it will be costly.
RNA seq will do better however the huge data set needs to be handled by an expert bioinformatation. KEEG analysis will give you the pathways and Denova assembly will provide you a lot of information
I think that your question about "good quality" is hard to answer before you perform the analysis. By RNA-Seq you will identified the differentially expressed genes across tissues. Those genes you can use to carry out a pathway analysis which potentially will provide you information about the biological processes that take place in each tissue. The complication that you have is that your organism is not sequence so the normal pipeline used in RNA-Seq is hard to apply.
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