Identify differentially expressed genes in scatter plot

Question

[woongjaej]

Hi, guys

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..

Woongjae

[cpad0112]

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

Answer 1

[Hussain Ather]

For making the scatter plot, check out ggplot in R or seaborn in Python. Those should let you highlight differentially expresssed genes as a different color in the plots.

[woongjaej]

Thanks for your reply Ather!

Is there any tutorials for such things using ggplot or seaborn, I can get the idea?