I'm new at analysing RNA-seq and I think I'm stuck so I wish to have some pointers from you experts. Sorry for the question if they are silly questions... What I want to do is draw a scatter plot for 2samples' differentially expressed genes form RNA-seq data(which has 3 replicates for each sample)
The questions are,
1.What value should I use for this kind of compare, if you recommend? Like FPKM, fold change, like that. 2.How can I merge the DEG results for each sample? 3.What is the best tool for this kind of scatter plot? 4.While making the scatter plot, I wonder if I can point out DEGs which I'm interested in, and color them different in the scatter plot.
Thank you for your kind replies..