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Old 02-08-2013, 08:13 AM   #1
stephenhart
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Location: Europe

Join Date: Sep 2011
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Question cummeRbund gene tracking

Hello,

I am having an issue with gene tracking in cummeRbund. The following happens:

> genetrack <- makeGeneRegionTrack(myGene)
Error in `[.data.frame`(features(object), , featCols) :
undefined columns selected

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.
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Old 03-14-2013, 11:43 AM   #2
adrian
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Hi:
any luck with
genetrack<-makeGeneRegionTrack(myGene)


> myGeneId<-"XLOC_000672"
> myGene<-getGene(cuff,myGeneId)

> head(features(myGene))
[1] feature_id gene_id isoform_id seqnames source type start end score strand frame
<0 rows> (or 0-length row.names)



In merged.gtf file obtained after cuffmerge, I find that the same gene/transcript exists.

chr1 Cufflinks exon 18164443 18164555 . - . gene_id "XLOC_000672"; transcript_id "TCONS_00000699"; exon_number "2"; gene_name "NM_001114847"; oId "NM_001114847"; nearest_ref "NM_001114847"; class_code "="; tss_id "TSS675"; p_id "P442";


In that case why I see features(myGene) is empty.

It is frustrating in deed.
-Adrian
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Old 03-14-2013, 12:00 PM   #3
adrian
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It works this way!!!!

cuff<-readCufflinks(gtfFile='myTranscriptome.gtf',genome='mm9',rebuild=T)



http://seqanswers.com/forums/showthread.php?p=85920
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Old 12-20-2014, 01:25 PM   #4
Gonza
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Hello Adrian, I am struggling with this too, does that mean you have to have the gtf file and the genome? Do you use genome.fa ? genome after you run bowtie-build?

Thanks
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