[BioC] Small RNA seq data analysis using DESeq

[Vedran Franke]

Dear Simon,

I have a question regarding the analysis of small RNAseq data using DESeq.
While counting the reads per loci I have weighted the reads by the
reciprocal of the places to which the read maps.
I was wondering whether it is still proper to use the negative binomial
test implemented in DESeq (after rounding the expression estimates) to
determine which loci are differentially expressed?

Best regards,

Vedran Franke