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The data I have: Two genotypes: wild-type (wt) and mutant (mut). Each genotype has RNA-seq data at 5 different time points. (t1, t2, t3, t4, t5) In total: about 18000 transcripts, 5 time points, 2 genotypes.
What I want to achieve: I want to identify all transcripts/genes with different kinetic trends in two genotypes. For example, gene A is stable from t1-t3 and then goes down in wt, but it stays stable across t1-t5 in mut.
One previous attempt: I wondered if I could convert the reads in t2-t5 into a fold-change over reads in t1, and then compare fold-change using DESeq2. But not sure if this is a valid data format for DEseqs.
Welcome all suggestions regarding how to achieve the desired comparison.
