DESeq2 q normalization RNA-seq and small RNA-seq

[RikyJKD]

Hi I have RNA-seq and small RNA-seq data and I would to compare the expression of the RNAs with the expression of the small RNAs. Is it correct if I used the DESeq2 normalization even if the data come from two different experimental protocols?
Thank you.

[blancha]

No, you are comparing apples and oranges.

The small RNAs are filtered out during the standard RNA-Seq protocol.
The small RNAs are selected during the small RNA-Seq protocol.
How then can you compare the counts from both libraries?

[RikyJKD]

I think you are right.
I have another doubt, using the example of apples and oranges, if I had the same organism but RNA seq of cell type A (apple) and RNA seq of cell type B (orange) would it be all right if i performed the differential analysis A vs B?
Thank you

[blancha]

Yes, with the caveat that both types of cells should produce the same amount of total RNA per cell, which is generally the case.

To understand the concept better, you should really think of read counts not as absolute values, but as proportions relative to the total amount of RNA sequenced.