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Old 06-26-2013, 12:45 AM   #21
ron128
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Quote:
Originally Posted by sdriscoll View Post
Looking at the dates of the questions, and the lack of responses, in this thread I get the feeling that the cufflinks developers are quietly waiting for people to stop using their tools. This combined with their google user group silence makes me wonder...is there a future for these tools?
Amen! Couldnt agree more!

IMHO though, Cufflinks-tophat is still a very viable option, inspite of the developers silence!
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Old 10-02-2014, 04:41 AM   #22
Gonza
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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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