(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.goe...@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.goe...@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
>>>>> ___________________________________________________________
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>>> <Presentation1.pptx>
>> 

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