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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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