I'm totally new in bioinformatics and have learned by myself with tuto's and guides during the last few months.
My experiment is a RNA-Seq profiling of diurnal cultures : I have 2 strains (WT and mutant) and 3 biological replicates for each, with sampling every 4h for 28h, which makes 8 time points (0 - 4 - 8 - 12 - 16 - 20 - 24 - 28). Thus making a total of 48 sets of data.
I already did the whole process of mapping the reads and counting them to end up with both raw counts and FPKM. I'm using the FPKM log2-fold change values with MapMan. And I have started to use the counts for a Differential Gene Expression analysis in R with DESeq2. My goal is to analyze how the transcriptome (17741 transcripts) is evolving during a day/night cycle but also to identify and analyze the differences between my 2 strains.
I already built the DESeqDataSets and DESeqResults with a complete design (design=~strain + time + strain:time) and with a reduced design : (design=~strain) or (design=~time) But that's where I'm a bit lost, despite reading any manual I could find. I don't get what I will get for results, what I should do with those values, how I can use them for graphics, how to chose which test is more relevant, ...
I probably didn't expose my situation clearly enough for you specialists, but any help would be so much appreciated!
Thanks already! Rémi