Hi. You can assume that 20% of the transcripts you have in your hands, if it 
is human data, will have antisense overlaps at 3'UTR or, to a lesser extent, 
to internal exons or 5'UTR

Since you can not distinguish this occurrence and you can not inroduce this 
correction factor in your datasets, you are left only with the option of 
summing all your tag (read) counts in my opinion.

A good, simple check would be to sample the distribution of - versus + 
strand matches - they should be around 50% each.

Hope this helps,

Alessandro

-----------------------------------------------------
Alessandro Guffanti - Bioinformatics, Genomnia srl
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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: wang peter <wng.peter@gmail.com>
 To: bioconductor@r-project.org
 Date: Mon, 23 Jul 2012 09:59:54 -0400
 Subject: [BioC] how to count for edgeR input


dear all:
        i have non-strand specific RNA-seq samples for
 edgeR analysis.
       first, i used bowtie to map my reads to the
 assembled contigs to count the sample. then for each
 contig, i got two number. one is forward count, the
 other is reverse count.
       if i sum these two number together to get one
 count number for edgeR input. is it right?
       should i sum them or average them

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