Hello everyone, I need a direction in using DEseq2.
my Input : I have RNAseq data from two groups of mice (groups based on type of bacterial treatment). Each group was harvested at 7 different time points. In other words I have two variable "type_of_bacteria" and "aging".
Upstream analysis done so far: pipeline 1: Fastq -> Kallisto-> tximport to input data to DEseq2
Alternate pipeline
Fastq -> Hisat2 -> HTseq2 -> tximport to input data to DEseq2
OUTPUT : to find the effect of bacterial treatment on the mice aging. i.e. Finding differentially expressed genes in response to bacteria in age-matched mice
Sample_Day1_type_A_bacteria vs Sample_Day1_type_B_bacteria
I have read old post related to this pos and thought to use design =( ~age+type_of_bacteria) but as you can see there are 7 aging time points, so this design might be useful.
Another option is subsetting the data but that might affect the normalization?
My lab is small so we not have statistician or person with bioinformatics background. any help is highly appreciated.
