Differential Expression Using mixed libraries (truseq, nextera)?

[feralBiologist]

I have 3 replicates for 2 conditions (6 samples) which have been sequenced using different protocols (nextera, truseq). Do I just need to use the library type as a blocking factor when defining the model for the differential expression?

I am planning to use edgeR but, I reckon, the same logic would apply to DESeq, too.

[dpryan]

Yes, just use library type as a factor.

[dpryan]

Also, cross-posted here.

[feralBiologist]

Yes, just use library type as a factor.

Thanks a lot!