Without seeing your data, it sounds as if the formatting of the file is corrupted. You may try using one of Galaxy's data transformation tools (GFF-to-BED) to see if that offers any clues, or a GFF or GTF file format validator (there are several offered online, I believe that UCSC also has one in their tool kit).
If this is direct output from Cufflinks, contacting the tool authors to ask if this is expected output is another good place to check. Contact information is in this section of our support wiki: http://wiki.g2.bx.psu.edu/Support#Unexpected_scientific_result
If all of this checks out, you may also want to contact UCSC to ask if there are any known limitations with display of RNA-seq data. As an alternative, the Trackster visualization tool in Galaxy has become quite robust with several new features and may be what you are looking for. It has been tuned to work particularly well with RNA-seq data (with both native and custom genomes). This would probably be my first choice as a test before going further. If Trackster produced an error with the dataset, then there is definitely a problem with formatting. If Trackster will display, then the problem may be with what UCSC is expecting and what Cufflinks is producing or with some post-Cufflinks processing.
Hopefully one of these will help discover the issue, but if you find that you are still stuck after working through the problem, please send a shared history link to email@example.com and we can try to provide feedback. Please include what you tested and the results so we are in the same place and know what is working and what isn't.
Going forward, please try to send new questions as brand new threads (not as replies to old threads with new subject lines) with the "to" address directly to firstname.lastname@example.org (you do not need to include me as a "to" or "cc"). This ensures that questions are not lost (as this one almost was) and that our entire team and community can contribute to and benefit from replies. I am sending this email now "to" galaxy-user to start up a new thread and correct the tracking. Replies should now be sent to this message as "reply-all". Thanks for understanding! Makes it much easier for us and nothing (well, we try!) slips through.
Jen Galaxy tem
Hi, I have generated a transcript file using cufflinks for the human (hg19) or zebrafish(zv9) assemblies. When I try to display the cufflinks "assembled transcripts" in UCSC I get this error in the UCSC browser and it wont display the transcripts.
human: GFF/GTF group NM_005638 on chrX+, this line is on chrY+, all group members must be on same seq and strand zebrafish: "GFF/GTF group vapb on chr6+, this line is on chr7-, all group members must be on same seq and strand"