Normalization in RNA Seq vs smallRNA

[anj_1]

Hello,

Trying to understand the best option for smallRNA normalization.

1) What are the main differences between normalization in smallRNA and mRNA?
2) What are the challenges smallRNA normalizatin pose which are not present in mRNA normalization?
3) What are the challenges that are present when you try to apply a certain normalization method that may work in mRNA but not in smallRNA? Why would they not work in smallRNA when they work fine in mRNA? Could you give an example?
4)Why is Quantile better than DESeq for smallRNA normalization? Is Lowess method as good as Quantile and if not why not?

Currently looking at the papers for DESeq and TMM and a few other articles on normalization. Trying to understand assumptions DESeq makes which would not work in smallRNA cases.

Thanks again!

[TiborNagy]

My opinion is smallRNA normalization is much easier, because smallRNAs are in a very small size range. The mRNA normalization is more challenging, because of different transcript sizes and alternative splice variants.
Most of the articles use only normalization to 1 million reads, but DESeq also can be used.