I've started learning RNA-seq only recently. I want to compare the DEG expression levels in WT(Wild Type) and three mutants(mutantA, mutantB, mutantC ; lacked a certain genes).
I tried to use hisat2, stringtie and ballgown(refer to https://www.nature.com/articles/nprot.2016.095). I've (probably) done these, but I don't know what to do next...
First of all, How to get DEG(diffentially expressed gene)?
I think that :
compare WT with mutantA
compare WT with mutantB
compare WT with mutantC
Merge there 3 results
I used TCC-GUI and carried out the above ,but I failed.
Will you kindly tell me how to get DEG and flow of making heatmap?
Thanks in advance for your help.