(cc'ing back to galaxy-user because this information may be useful to others)
The problem is that the reference gene annotation that you're using, RefGene from UCSC, has an error. Specifically, a transcript_id attribute is duplicated for two different transcripts, one on chr1 and one on chr19:
-- chr1 Cufflinks transcript 34611 36081 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr1 Cufflinks exon 34611 35174 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr1 Cufflinks exon 35277 35481 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr1 Cufflinks exon 35721 36081 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "3"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr19 Cufflinks transcript 76220 77690 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr19 Cufflinks exon 76220 76783 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr19 Cufflinks exon 76886 77090 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr19 Cufflinks exon 77330 77690 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "3"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; --
When trying to visualize either the reference annotation or Cufflinks datasets created using this annotation, an error occurs because Galaxy tries to reconcile these two transcripts. More graceful error handling is planned.
To avoid this error, use the iGenomes reference available in the iGenomes data library (hg19 and mm9 only right now). There are other benefits to this annotation as well; it has additional attributes useful for Cuffdiff. I was able to visualize your Cufflinks data, as well as the iGenomes gene annotation, using Trackster.
Best, J.
On Nov 2, 2012, at 7:16 PM, i b wrote:
On Fri, Nov 2, 2012 at 12:33 PM, Jeremy Goecks jeremy.goecks@emory.edu wrote:
Please share the history with me and I'll take a look.
Thanks, J.
On Nov 2, 2012, at 4:54 AM, i b wrote:
Hi Jeremy, I was trying to visualize "assembled transcripts". none of these works from any of my jobs.
The line where I should see the assembled transcript is empty and you can click on "visualize error". I have attached what the error says, If I click "try again", after a while it comes out the same view (the lien describing view error and try again)
thanks for your help, ib
On Fri, Nov 2, 2012 at 12:58 AM, Jeremy Goecks jeremy.goecks@emory.edu wrote:
I'm able to visualize Cufflinks assembled transcripts in Trackster. Can you please be more specific about (a) which datasets you're having trouble using and (b) what errors you're seeing?
Thanks, J.
On Oct 31, 2012, at 1:10 PM, i b wrote:
Hi all, can anyone explain me wh how can I visualize cufflinks outputs in trackster? galaxy keep sending me errors
thanks, ib ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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Jeremy Goecks