Hi, I am trying to perform a differential seq analysis using DESeq2 package. I have data from 16 cell lines (Control and knockdown of a gene of interest). The issue is that library prep for 16 cell lines wasn't performed in the same batch. We performed library prep for 8 cell lines (equal distribution between control and knockdown) and then performed another "batch" of library preps for next 8. The library prep method was the same. They were sequenced on the same sequencing run.

My question is, while running DESeq2, should I be accounting for potential "batch effects" arising out different library preps days ?

Code should be placed in three backticks as shown below

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

Yes. You should be accounting for it. Library prep day matters. Sequencing day does not. Just make your design ~ genotype + batch