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):
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):
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.