Question: Cuffdiff gene ID
gravatar for Fang,Xiefan
3.2 years ago by
United States
Fang,Xiefan30 wrote:

I am using galaxy for differential gene expression analysis. I first converted the ensembl GTF file by using the "Make Ensembl GTF compatible with Cufflinks" workflow. I used the converted annotation file for cufflinks and cuffmerge analysis, followed by cuffdiff. I noticed that the gene_id was changed to XLOC IDs instead of Ensembl IDs (see below). How can I keep the ensembl ID for genes and transcripts? Thank you very much!!

For transcript differential expression testing:

test_id gene_id gene locus
TCONS_00000001 XLOC_000001 RP23-271O17.1 chr1:3073252-3074322
TCONS_00000002 XLOC_000002 Gm26206 chr1:3102015-3102125
TCONS_00000003 XLOC_000003 RP23-317L18.1 chr1:3205900-3671498
TCONS_00000004 XLOC_000004 Gm1992 chr1:3205900-3671498
TCONS_00000005 XLOC_000005 RP23-115I1.2 chr1:3205900-3671498


For gene differential expression testing:

test_id gene_id gene locus
XLOC_000011 XLOC_000011 RP23-37D15.2 chr1:4610470-4611406
XLOC_000057 XLOC_000057 Gm26348 chr1:10137570-10232670
XLOC_000139 XLOC_000139 Khdc1b chr1:21383555-21386373
XLOC_000152 XLOC_000152 RP23-255J24.2 chr1:24100624-24103424
XLOC_000174 XLOC_000174 Gm29128 chr1:31135225-31222684
gff cufflinks galaxy • 2.9k views
ADD COMMENTlink modified 3.2 years ago by Jennifer Hillman Jackson25k • written 3.2 years ago by Fang,Xiefan30

Hi, Did you find any solution for this? I am also facing the same problem? Did iGenome version made any difference?

ADD REPLYlink written 15 months ago by sreerajthamban160
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The attributes in the input annotation dataset (GTF/GFF3) make a big difference is how Cufflinks/Cuffdiff functions. Using the iGenomes ( version is the recommendation, if available for your genome. 

For more about the expected inputs for this tools and how attributes are used, please see the manual here (the clearest, most current usage is explained):

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 8 weeks ago • written 3.2 years ago by Jennifer Hillman Jackson25k
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