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!
1 answer
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.
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