Hi 

I have read counts (based on multiple mapping) for small RNAs. Since it is normalized for multiple mapping, some of the read counts have decimalized values on which I would like to perform differential expression (condition A vs B). 

My specific question is if edgeR accept decimal / integer read counts for differential expression ?

Best regards

Paddy

Yes it does. All the edgeR analysis pipelines accept fractional counts. edgeR uses a continuous version of the negative binomial distribution so that it can work directly with fractional counts without rounding them to integers.