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Old 10-02-2014, 03:41 AM   #22
Gonza
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Location: Ithaca, NY

Join Date: Mar 2013
Posts: 78
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Dear All,

Basic question. I run tuxedo without using cuffcompare. Used tophat2 --> cufflinks --> cuffmerge --> cuffdiff --> R.
Data looks good, makes sense. However, I cannot figure out how to have access to 8.1.1 Gene Feature plots (http://compbio.mit.edu/cummeRbund/manual_2_0.html)

For example, I do :

myGeneId<-"XLOC_012114"
myGene<-getGene(cuff_data,myGeneId)
myGene
XLOC_012114 <-expressionPlot(myGene)
XLOC_012114

head(fpkm(myGene))
head(fpkm(isoforms(myGene))) # up to here all works

head(features(myGene))# not working yet
genetrack<-makeGeneRegionTrack(myGene) # not working yet
plotTracks(genetrack) # not working yet

Is this because i did not use cuffcomare? should I rerun the analysis? Is that critical to use cuffcompare?

Please let me know what you think
Thanks in advance
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