My experimental setup contains two Arabidopsis thaliana ecotypes (Col-0 and Bur-0) that are infected either with a virus or mock. I want to compare the response of these two genotypes to virus infection at the transcript level by RNA-seq. My problem is that although these ecotypes are closely related, they still have plenty of differences: mutations that can cause amino-acid changes in the coded proteins, rearranged/fused genes, novel alternative transcripts, etc. This means that the reference transcriptome for the alignment will be different.
Which of the following approaches do you think is the best?
I appreciate any suggestions.
Peter,
Based on everything I know about Arabidopsis thaliana ecotype Col-0, I would say that Col-0 has quite different biochemistry comparing to Bur-0, and it would probably explain high frequency of diverse resistances in this ecotype. I think your #2 followed by #5 is reasonable way.
Alex
Hi Alex,
Thank you for the answer, I also prefer the #2, but I think I will try a few approaches and see what I get.
Cheers,
Peter
Thank you Ali, actually I realized that I did not make it clear in my question that I want to investigate the transcriptome by NGS (RNA-seq). I edited the question accordingly.
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