Hi - it the same miRNA read maps to three different location in the genome, 
it is indeed
a fact a little bit against your smallRNA being an actual miRNA

I would name each match with chr:start-end and count +1 for each location

My two cents

Alessandro

-----------------------------------------------------
Alessandro Guffanti - Bioinformatics, Genomnia srl
Via Nerviano, 31 - 20020 Lainate, Milano, Italy
Ph: +39-0293305.702 Fax: +39-0293305.777
http://www.genomnia.com
"If you can dream it, you can do it" (Walt Disney)

-----Original Message-----
 From: Mete Civelek <mcivelek@mednet.ucla.edu>
 To: <bioconductor@r-project.org>
 Date: Mon, 21 May 2012 12:24:43 -0700
 Subject: [BioC] non-integer counts for edgeR


Dear All,

 I am analyzing microRNAseq data with edgeR. Because some of the reads map 
to
 multiple locations, I weighed the counts based on the number of genomic
 locations that a read maps. For example, if a read maps to 3 locations, 
each
 location gets a count of 1/3. Of course, this means that the read counts 
for
 some miRNAs in some samples are not integers. Is it possible to use these
 counts to do differential expression analysis with a quantitative trait in
 edgeR? My understanding is "no" but I thought someone can suggest a
 solution.

 Thank you for your help.

 Best Regards,

 Mete

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