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Old 02-24-2013, 12:35 AM   #1
Location: Europe

Join Date: Sep 2011
Posts: 16
Default gene tracking in cummeRbund


I am having difficulty with the makeGeneRegionTrack command in cummeRbund. Below is what happens, after rebuilding the cuffData.db with the gtf file downloaded from the cufflinks website. I'd appreciate any advice on what the problem might be. I've had no problems operating any other cummeRbund commands, so might data is presumably is sufficient and uploaded correctly.


> cuff <- readCufflinks(genome='mm10',gtfFile='genes.gtf',rebuild=TRUE)
Creating database /Users/myfolder/Desktop/cuff_results/cuffdiff/cuffData.db
Reading Run Info File /Users/myfolder/Desktop/cuff_results/cuffdiff/
Writing runInfo Table
Reading Read Group Info /Users/myfolder/Desktop/cuff_results/cuffdiff/
Writing replicates Table
Reading GTF file
Writing GTF features to 'features' table...
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Writing geneData table
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/gene_exp.diff
Writing geneExpDiffData table
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/promoters.diff
Writing promoterDiffData table
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/genes.count_tracking
Reshaping geneCount table
Writing geneCount table
Reading read group info in /Users/myfolder/Desktop/cuff_results/cuffdiff/genes.read_group_tracking
Writing geneReplicateData table
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/isoforms.fpkm_tracking
Checking samples table...
Writing isoforms table
Reshaping isoformData table
Writing isoformData table
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/isoform_exp.diff
Writing isoformExpDiffData table
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/isoforms.count_tracking
Reshaping isoformCount table
RecastingWriting isoformCount table
Reading read group info in /Users/myfolder/Desktop/cuff_results/cuffdiff/isoforms.read_group_tracking
Writing isoformReplicateData table
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/tss_groups.fpkm_tracking
Checking samples table...
Writing TSS table
Reshaping TSSData table
Writing TSSData table
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/tss_group_exp.diff
Writing TSSExpDiffData table
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/splicing.diff
Writing splicingDiffData table
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/tss_groups.count_tracking
Reshaping TSSCount table
Writing TSSCount table
Reading read group info in /Users/myfolder/Desktop/cuff_results/cuffdiff/tss_groups.read_group_tracking
Writing TSSReplicateData table
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/cds.fpkm_tracking
Checking samples table...
Writing CDS table
Reshaping CDSData table
Writing CDSData table
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/cds_exp.diff
Writing CDSExpDiffData table
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/cds.diff
Writing CDSDiffData table
Reading /Users/myfolder/Desktop/cuff_results/cuffdiff/cds.count_tracking
Reshaping CDSCount table
Writing CDSCount table
Reading read group info in /Users/myfolder/Desktop/cuff_results/cuffdiff/cds.read_group_tracking
Writing CDSReplicateData table
Indexing Tables...

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

The database appears to be successfully built. I then make and call my gene of interest:

> head(features(myGene))
seqnames start end width strand source type score
1 chr12 55598917 55602017 3101 + unknown exon NA
2 chr12 55599473 55600951 1479 + unknown CDS NA
3 chr12 55599473 55599475 3 + unknown start_codon NA
4 chr12 55600952 55600954 3 + unknown stop_codon NA
phase gene_id isoform_id gene_name CDS_id TSS_group_id
1 NA Insm2 NM_020287 Insm2 P1443 TSS20567
2 0 Insm2 NM_020287 Insm2 P1443 TSS20567
3 NA Insm2 NM_020287 Insm2 P1443 TSS20567
4 NA Insm2 NM_020287 Insm2 P1443 TSS20567

When I then try to make the gene region track, I get the following:

> genetrack <- makeGeneRegionTrack(myGene)
Error in `[.data.frame`(features(object), , featCols) :
undefined columns selected
stephenhart is offline   Reply With Quote
Old 03-19-2013, 12:09 PM   #2
Location: Freiburg

Join Date: Oct 2012
Posts: 56

I am experiencing exactly the same problem. And I am using the exactly same gtf file as I used for cuffdiff.
DonDolowy is offline   Reply With Quote

cummerbund, gtf, mm10

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