[BioC] Exonic part number of genes on the reverse strand

[Conan [guest]]

  Hi all, I have a simple question when using plotDEXSeq to visualize DEXSeq’s result.
  When a gene is on a reverse strand, its first exon's coordinate should be larger than the last exon’s. Just as Fig3 in paper “Detecting differential usage of exons from RNA-seq data”, gene FBgn0004449 is on reverse strand and the plot result shows that exonic part number is aggregated from right to left (bigger coordinate to smaller). But in vignette of DEXSeq for version 1.6.0, the example gene used for plot, FBgn0010909, is also on negative strand but the exonic part number 1 starts from leftmost. For me I think first consequence is better to help me corresponding the exonic part to the exon number of a candidate gene, but my plot result is kind of the latter. 
  Is there any way to fix this? I think it’s when dexseq_prepare_annotation.py dealing with gtf files it neglected the gene's strand information so all gene's exonic part number was aggregated from smaller coordinate am I right?


 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

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

other attached packages:
[1] BiocInstaller_1.10.1 DEXSeq_1.6.0         Biobase_2.20.0       BiocGenerics_0.6.0  

loaded via a namespace (and not attached):
 [1] biomaRt_2.16.0       Biostrings_2.28.0    bitops_1.0-5         GenomicRanges_1.12.4 hwriter_1.3          IRanges_1.18.1       RCurl_1.95-4.1       Rsamtools_1.12.3    
 [9] statmod_1.4.17       stats4_3.0.1         stringr_0.6.2        tools_3.0.1          XML_3.96-1.1         zlibbioc_1.6.0     

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