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.
> 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