Question: Problem when running read cufflinks
gravatar for PRJNA348534
15 months ago by
PRJNA3485340 wrote:

getting problem the running

readCufflinks(gtfFile = "Galaxy802-merged_transcripts.gtf", runInfoFile = "", repTableFile = "", geneFPKM = "genes.fpkm_tracking", geneDiff = "gene_exp.diff", geneCount="genes.count_tracking.tabular", geneRep="genes.read_group_tracking.tabular", isoformFPKM = "isoforms.fpkm_tracking", isoformDiff = "isoform_exp.diff", isoformCount="isoforms.count_tracking file.tabular", isoformRep="isoforms.read_group_tracking.tabular", TSSFPKM = "tss_groups.fpkm_tracking", TSSDiff = "tss_group_exp.diff", TSSCount="tss_groups.count_tracking file.tabular", TSSRep="tss_groups.read_group_tracking.tabular", CDSFPKM = "cds.fpkm_tracking", CDSExpDiff = "cds_exp.diff", CDSCount="cds.count_tracking file.tabular", CDSRep="cds.read_group_tracking.tabular", CDSDiff = "cds.diff", promoterFile = "promoters.diff", splicingFile = "splicing.diff", driver = "sqlite", genome = "Glycine_max.V1.0.dna.toplevel.fasta", rebuild = T,verbose=F )

Creating database /Users/apple/Documents/R_analysis/cuffData.db Reading Run Info File /Users/apple/Documents/R_analysis/ Writing runInfo Table Reading Read Group Info /Users/apple/Documents/R_analysis/ Writing replicates Table Reading GTF file Writing GTF features to 'features' table... Reading /Users/apple/Documents/R_analysis/genes.fpkm_tracking Checking samples table... Populating samples table... Error: Column name mismatch. In addition: There were 50 or more warnings (use warnings() to see the first 50)


ADD COMMENTlink modified 7 weeks ago by Jennifer Hillman Jackson25k • written 15 months ago by PRJNA3485340

Any resolution to this? Getting the same error.

ADD REPLYlink written 7 weeks ago by sdbaney10
gravatar for Jennifer Hillman Jackson
7 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:


This issue was a genome mismatch problem between the reference genome and the reference annotation.

To resolve similar problems, please see the FAQs here:

Also -- Tophat and all Cuff* tools are older. Current RNA-seq tools/methods are covered in the Galaxy tutorials.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 weeks ago by Jennifer Hillman Jackson25k
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