Hello, It is my first time doing dual rna-seq DEG analysis and am a bit lost. I have a table with read counts for various time points and cell lines and two conditions (infected vs uninfected) for both the parasite and the host (human). I have been using deseq2 for the analysis. Specifically, I am trying to focus on one single time point and a single cell line. I have a data frame in R and extracted only those count reads from my table matrix, then I set up the design and got the fold change.
However, I am doing something wrong because I can't seem to replicate the results as expected (paper below). Any ideas what am I doing wrong? Do I need to do an additional comparison for read counts in the parasite and the host read counts?
This is the paper I am using as base: https://www.nature.com/articles/s41467-019-08349-0 (Figure 1a-b)
Thank you!
Hello, I think at this point it is hardly possible to give specific advise. Try to be more focused, e.g. by showing some code. Right now we have no idea what exactly you did, which results were expected and which results you got.