RNAseq data with no replicates.What novel or different analysis can be done??

Question

[ppnana]

I have a plant transcriptome data with no biological replicates.i have done annotation.I cannot do differential analysis.What more or new can be done?somebody suggest?? Is finding SNP is useful? Kindly suggest

[ATpoint]

I find it strange that you ask the community what can be done. Actually, you should know what scientific question you want to answer, then asking for help HOW (not what) this can be accomplished. So what is the purpose and goal of your work?

[Mehmet]

It depends on what you want to find. You can perform differential gene expression analysis if you have two different transcriptome assembly (you can use the tool gfold). For more analyses, you can focus on biology of the plant species and therefore you can do more deep analyses depending on biology, ecology etc. of the plant species. For example, if the plant species is a drought resistant species, you can search LEA (late embryogenesis abundant) proteins, and compare other plants or organisms to see whether it is conserved or not in your species or how it is divergent, or if the plant species distribute in some soil conditions (some heavy metals etc.), you can search resistant related genes. If the plant species is under threat due to several pathogen, you can search pathogen recognization proteins in your species etc. Further analyses depend on what you want to do :)

[ppnana]

thanks mehmet

I have a plant whose metabolite is used as a drug.Can you suggest what exactly ca be done

[Mehmet]

First, do a deep search on the literature to see which disease or pathological agent the plant species is used as a drug. Try to find immunological proteins of the plant species, and depending on the drug, you can search motifs of candidate proteins that are associated with "binding function". Compare your results with proteins of other species that are used as drug. You can suggest "candidate" drug-related proteins. But keep in your mind when it comes to "drug", there is much more complicated process. All you can do with transcriptome data only is to suggest candidate proteins, which is also quite complicated because of lack of "candidate" drug targets. For instance, which molecules can be targeted to use your species results as a drug, and what their molecule structure? These topics are more related to organic chemistry rather than Bioinformatics. These are my opinion. Try to do your best. Search the literature, follow tools/programs to analyze, and ask people here if you need help.