I am trying to analyze co-transcriptome data from two enteric pathogens. These are new clinical isolates (X and Y). I have RNASeq reads from each species grown individually (X or Y) and from the co-growing culture (X+Y). The pattern of growth observed in in vitro cultures is that X suppresses growth rate of Y and we are trying to have a mechanistic explanation for this pattern.
For this, I used trinity for de novo transcriptome assembly and then RSEM (as an example of alignment based) or Kallisto (as an example of alignment-free). I then ran DESeq2 on the read counts from both RSEM and Kallisto and compared the differentially expressed genes from each case.
I get contradicting results when using both methods: using RSEM: > 2000 genes are sig up regulated in co-growth X+Y culture relative to individually grown X and < 100 down regulated. using Kallisto: > 1500 gene are sig down regulated in co-growth X+Y culture relative to individually grown X and ~300 are up regulated.
Also the skew in the number of DEG towards being up/down regulated is a bit suspicious.
My question is which method should I follow in this case ? What is a good approach for analyzing RNASeq from such an experimental setup ?
Any insights or help will be highly appreciated Thanks