What Statistical Test Is Appropriate When Comparing Rna-Seq Data Obtained From Biological Replicates Mapped To Different Genomes

Question

[xs57]

Hi, all

I have two groups of RNA-seq data (A and B), with both two biological replicates within groups(A1, A2 and B1, B2). For each replicate, the reads are mapped two genomes(X,Y). Now I have counted the mapped reads for each orthologs between X and Y. Next, I want to do statistic test on expression ratio of X/Y between groups. I don't know which model or method could be used, anyone who can give suggestions. Thanks

[Damian Kao]

I am not sure how valid your expression data will be if you are mapping reads from one organism to a different genome.

[xs57]

Sorry for not clearly explained, the data of each replicate are the mixture of gDNA from closely related species. Actually, the group A is the mixture of gDNA haploid X and haploid Y. The B is the diploid cell with genome X and Y.

[Damian Kao]

So this is genomic DNA?

[xs57]

No, this is cDNA data. I can make it more clearly so somebody else may have suggestions. We have two haploid cell X and Y, and their hybrid XY (diploid genome). Now we got the RNA from co-cultured X and Y (group A), as well as the single culture XY (group B). Because X and Y are closely related, so we can get the orthologs and count the reads in each group. Next step, I want to know, for a giving orthologous gene, whether the expression ration (X/Y) are different between group A and gourp B (each group has two replicates). I hope it will get you better understood.