Question: Cummerbund Gene Tracking
1
gravatar for Eric
6.3 years ago by
Eric90
Eric90 wrote:

Hello,

I am having an issue with gene tracking in cummeRbund. Here is the cuff output:

>     cuff
CuffSet instance with:
     4 samples
     23285 genes
     30073 isoforms
     25872 TSS
     24748 CDS
     139440 promoters
     155232 splicing
     122340 relCDS

But when I try to run gene tracking, the following happens:

> myGeneId <- "ENSMUSG00000045440"
> myGene <- getGene(cuff,myGeneId)
> myGene
CuffGene instance for gene ENSMUSG00000045440 
Short name:     ENSMUSG00000045440 
Slots:
     annotation
     features
     fpkm
     repFpkm
     diff
     count
     isoforms     CuffFeature instance of size 1 
     TSS         CuffFeature instance of size 0 
     CDS         CuffFeature instance of size 0 
> genetrack <- makeGeneRegionTrack(myGene)
Error in `[.data.frame`(features(object), , featCols) : 
  undefined columns selected

Therefore, I'm unable to visualize transcript-level features of my gene of interest. I am using an Ensembl gtf and have set

> options(ucscChromosomeNames=FALSE),

but no luck. I have also tried using the cummeRbund cufflinks data from the sample directory

a<-readCufflinks(system.file("extdata", package="cummeRbund"))

but still no luck. I have no issue analyzing 'myGene' or any other cummeRbund feature, so I assume I've accessed the data correctly. Any ideas on what the problem might be?

Thanks.

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Eric90

If you post your entire R script as well as explain what you expected to happen, that would be helpful.

ADD REPLYlink written 6.3 years ago by Matt Shirley9.0k

have you tried using the recommended genes.gtf file downloable from the Tuxedo package website?

ADD REPLYlink written 6.3 years ago by GPR310
0
gravatar for Matt Shirley
6.3 years ago by
Matt Shirley9.0k
Cambridge, MA
Matt Shirley9.0k wrote:

You might take a look at this post on SEQanswers. You still did not post your entire R script, as we do not know what your cuff data frame looks like, and I suspect that your issue arises because your are not reading into R the proper GTF output from cufflinks.

ADD COMMENTlink written 6.3 years ago by Matt Shirley9.0k

@Matt I've now included the cuff output in the post - I think this is what you were looking for.

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by Eric90
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