Hi from Montpellier (France)
Dear SEQanswers community,
I a postdoc working on Rice and its pathogen Magnaporthe.
I have just started RNAseq project to look at differentially expressed genes during infection and different treatments.
I am interested in both, the Rice and Magnaporthe genes.
Perhaps the question (below) was already asked, so I will try to find existing answers on the forum. If not here it is:
I will have 20M reads (1x50bp) for non infected samples and 60M reads for samples infected with Magnaporthe. Apparently, different number of reads can cause some bias/analysis problems.
What is the best method to look at differentially expressed genes between those samples?
I would be very happy if you could help with my question. Thanks for your help!
Cheers,
Przemek
I a postdoc working on Rice and its pathogen Magnaporthe.
I have just started RNAseq project to look at differentially expressed genes during infection and different treatments.
I am interested in both, the Rice and Magnaporthe genes.
Perhaps the question (below) was already asked, so I will try to find existing answers on the forum. If not here it is:
I will have 20M reads (1x50bp) for non infected samples and 60M reads for samples infected with Magnaporthe. Apparently, different number of reads can cause some bias/analysis problems.
What is the best method to look at differentially expressed genes between those samples?
I would be very happy if you could help with my question. Thanks for your help!
Cheers,
Przemek