rna seq matrix design hybrids

Question

I am struggling to get my head around the correct design to use for my experiment. I have RNAseq of 2 pure species (s1, s2) and of the hybrid (h). I aligned all three genotypes to the s1 genomes. I am interested in the comparison of hybrids vs s1 (maternal genome). But I want to remove a potential bias from reads from s2 chromosome being harder to align to s1. (The hybrid genome is composed of both s1 and s2.) I would like to correct my DE test by removing potential effect s2 vs s1. (I aligned s2 to s1 and got the count.) But my issue is, I fail to have a full rank design. I do not have any strong feelings about the library (deseq2, edgeR...).

Following the tutorial

below is the condition matrix, as you can see if I want to make the contrast ~ s2 + condition. The matrix is not full rank. I believe I could write my design as ~s2 + h - s1 ?? But I don't know how to use deseq2 for this approach.

Any approach/tips to achieve my goal here? Is it event possible? what

sample	condition	s2
1	s1	0
2	s1	0
3	s1	0
4	s2	1
5	s2	1
6	s2	1
7	h	0
8	h	0
9	h	0

any help is warmly appreciated!

Answer 1

I think you are over thinking the problem. You need to classify the genes of interest and to do that a classifier such as eggNOG is used. This will remove any bias. I understand eggNOG because it's based on protein phylogenetics and phylogenetics is what I do and I can assure you its very solid and the algorithm nicely constructed.

DESeq2 (I ain't a huge fan BTW, but avoid controversy) will happily accept eggNOG classification, here

Then its simply three tests

1. S1 vs S2
2. S1 vs hybrid
3. S2 vs hybrid

I personally would perform unsupervised learning, particularly via Scanpy first on S1, S2 and hybrid separately. This will give a rough indication of the key difference of expression profiles between S1 and S2 and see where the hydrid occurs.