Gene Tracking In Cummerbund

Question

[Eric]

Hello,

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've had no problems operating any other cummeRbund commands, so might data is presumably is sufficient and uploaded correctly.

I have previously posted on this problem (Cummerbund Gene Tracking), but the following is after incorporating the recommended genes.gtf file from the tuxedo website.

I'd appreciate any advice on what the problem might be.

Thanks, SH

> 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/run.info
Writing runInfo Table
Reading Read Group Info  /Users/myfolder/Desktop/cuff_results/cuffdiff/read_groups.info
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
Recasting
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
Recasting
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...
OK!
Writing isoforms table
Reshaping isoformData table
Recasting
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...
OK!
Writing TSS table
Reshaping TSSData table
Recasting
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
Recasting
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...
OK!
Writing CDS table
Reshaping CDSData table
Recasting
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
Recasting
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

[Fred De Masi]

Hi Eric,

Did you ever manage to solve this issue?

Cheers,

Fred