Question: What Statistical Test Is Appropriate When Comparing Rna-Seq Data Obtained From Biological Replicates Mapped To Different Genomes
gravatar for xs57
8.0 years ago by
xs5720 wrote:

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.

bioinformatics rna-seq • 2.3k views
ADD COMMENTlink modified 2.1 years ago by Biostar ♦♦ 20 • written 8.0 years ago by xs5720

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

ADD REPLYlink written 8.0 years ago by Damian Kao15k

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.

ADD REPLYlink written 8.0 years ago by xs5720

So this is genomic DNA?

ADD REPLYlink written 8.0 years ago by Damian Kao15k

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.

ADD REPLYlink written 8.0 years ago by xs5720
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