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..
FPKMs are not comparable between sample AFAIK, Probably this would help: https://www.reddit.com/r/bioinformatics/comments/3mmezs/comparing_fpkm_between_samples/