[BioC] Exonic part number of genes on the reverse strand
guest at bioconductor.org
Sat Jun 8 18:12:30 CEST 2013
Hi all, I have a simple question when using plotDEXSeq to visualize DEXSeqâs result.
When a gene is on a reverse strand, its first exon's coordinate should be larger than the last exonâs. Just as Fig3 in paper âDetecting differential usage of exons from RNA-seq dataâ, 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 itâs 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():
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
 LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
 LC_TIME=English_United States.1252
attached base packages:
 parallel stats graphics grDevices utils datasets methods base
other attached packages:
 BiocInstaller_1.10.1 DEXSeq_1.6.0 Biobase_2.20.0 BiocGenerics_0.6.0
loaded via a namespace (and not attached):
 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
 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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