How can I analyze more than two conditions in DESeq2?

Question

[Lila M]

Hi, I'm stuck analyzing a data set of genes that corresponds to different timepoints. I used DESeq for this approach but in that case I have different condition :

data file
ID  time        
14h_S1.bam  14h 
14h_S7.bam  14h 
16h_S2.bam  16h 
16h_S8.bam  16h 
19h_S3.bam  19h 
19h_S9.bam  19h 
22h_S4.bam  22h         
22h_S10.bam 22h 
24h_S5.bam  24h         
24h_S11.bam 24h 
28h_S12.bam 28h 
28h_S6.bam  28h

So the time is the hours after an specific treatment. As I want to know the genes deferentially expressed and the counts for those genes, Can I use DESeq2 after feature counts (that works fine for two conditions) or should I use another package? Many thanks!

Answer 1

[Lisa Ha]

You can definitely use DESeq2 for that. The vignette even has a section on different ways of analysing time-series data with DESeq2. DESeq2 vignette. Which approach you use depends on your biological question though, which isn't clear from your question. You can also find an example workflow here.