Hello, 

I have set a UCSC trackhub, which includes annotations that were originally in the GTF or GFF formats. So I followed the steps described here: https://genome.ucsc.edu/goldenPath/help/bigGenePred.html (example 4: GTF (or GFF) to BigGenePred) to obtain a binary bigGenePred for each GTF / GFF. 

It works fine, except that when visualizing the result, I loose data on introns and strand orientation. It means that for each gene annotated, I get a solid line, going from the 5' end to the 3'end of the gene.

One example of what I get (the first 3 light blue top lines are from one of my GTF annotation turned to binary bigGenePred):

![Track hub screen capture][1]

I really want to see a finer granularity where you can actually see exons / introns and strand orientation, so I tried to upload one of my GTF to a custom track. This way works: I do not lose data from the annotation and get to see all the details. However, I could not find a way to integrate a custom track to a track hub. 

Result with the custom track (top 3 black lines are from one of my GTF annotation):
![Custom track screen capture][2]

So this my question: what is the best way to integrate a GTF file to a trackhub and not lose any detail ? 

Thanks for the help.


  [1]: https://i.ibb.co/zsqHPKL/Capture-d-e-cran-2020-05-20-a-11-30-05.png
  [2]: https://i.ibb.co/mGrVvrD/Capture-d-e-cran-2020-05-20-a-11-45-05.png
Glad it was solved! I'm just going to copy the response as an answer so the post doesn't show up unanswered:

Hello,

bigGenePred does support intron/strand information. It should not be a problem when converting from a GTF/GFF. Initial suspicions are the problem may be the way the trackDb stanza is declared in the hub. Are you stating type bigGenePred, etc? Another possibility could be the input GTF file or the conversion (stating the correct bidBed 12+8), but that's less likely. Essentially from your first screenshot it looks like the Genome Browser is displaying your file as a BED3.

If you would like to email us a copy of the GTF file as well as a link to the hub to our private mailing list (genome-www@soe.ucsc.edu) we could take a look. Note that only internal Genome Browser staff can see the contents of the message.