Hello, 

I analyzed my RNAseq data with DESeq2 and currently I am trying to use it for the differential accessability estimation for ATACseq data. 

However, I am not sure If I have made right design. I am sorry if this question hawe been asked before. 

I want to perform Diff Exp/ Diff Access between Control and Disease,  However, for ATAC seq data it is important to add gender as posible confounding factor, so code I wrote:

design(DDS) <- ~ SEX + Condition
DDS  <- DESeq(DDS)
results.DDS <- results(DDS, contrast = c("Condition", "Mild_disease" , "Control"))

Will my selected design take in account possible gender effect on genes/regions called significant?                                  

Kind Regards 

Yes, that is how to control for sex while testing on condition differences. I think it's important with ChIP or ATAC to look at the MA plot and make sure the normalization makes sense for your data (e.g. is there a cloud of points clearly centered on y=0).