Analyzing time-series RNA-seq data using DEseq2

Analyzing time-series RNA-seq data using DEseq2

1

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.


DEseq2


data


RNAseq


Sleuth


analysis

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