[BioC] .wig files for strand-specific paired-end RNA-Seq

[Igor Ulitsky [guest]]

Hi,

Is there a simple way to make strand-specific .wig file (i.e., a separate track for + and - strand) from paired-end data (where the second read maps to the other strand)? I've tried using this:

library(Rsamtools)
library(rtracklayer)
myReads <- readGappedAlignments("RNAseqMapping.bam")
coveragePlus <- coverage(myReads[strand(myReads) ==  '+'])
export(coveragePlus, "RNAplus.wig")
coverageMinus <- coverage(myReads[strand(myReads) ==  '-'])
export(coverageMinus, "RNAminus.wig")

But it appears that the second read in the pair contributes to the other strand, generating similar tracks for the + and the - strands.
Is there a way to deal with this better?

Thanks!

Igor. 

 -- output of sessionInfo(): 

R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_2.13.1

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