Entering edit mode
23 months ago
Hi! I'm working with RNAseq data. I have 3 tissue-especific D. melanogaster: Muscle, Imaginal wing disc and Fat body.
I want to compare the tissues between each other to find the common and specifics differential expressed genes, but I don't know what is the best way to compare them.
Any suggestions would be very helpful.
How many samples per group?
There are many options, and which one best suits you depends on your prior knowledge and access to computing infrastructure (e.g. tools might vary in regard to their memory demands). If the data is already processed until the stage of gene / transcript counts, try Degust first, since you can use it in the browser with a graphical user interface. If you know how to code R, you can run edgeR directly to have better control and reproducability.
If your data is basically fresh off the sequencer, run the nf-core RNA-seq pipeline first to process the data to gene / transcript counts.