Hi Eric,
To go back to the original issue with the BED tracks not correctly
display the strand indicator arrows, we believe that this is a bug and
will look into it. Unfortunately, I can't offer a timeframe for when
this will be fixed.
I'm not sure why the strand arrows don't show up for your genePred
track. Perhaps you have the "codon coloring" (or codon translation)
option turned on? If you have this option turned on and there are no
introns in your annotations, then no strand arrows will be displayed.
One of our engineers notes that while it's possible to get this sequence
information into genePred tables, that it is much easier to just use the
new "bigGenePred" file format. These "predicted mRNA" and "translated
protein from predicted mRNA" links should be present on the details
pages of bigGenePred tracks. The bigGenePred file format does work for
native tracks as well. You can find instructions on creating your own
bigGenePred files here:
https://genome.ucsc.edu/goldenPath/help/bigGenePred.html. To use these
for native tracks, all you need to do is add a "bigDataUrl" line to the
stanza that points to the file. The information on this bigDataUrl line
can just be a relative path to the file on your machine.
I hope this is helpful. If you have any further questions, please reply
to
genome...@soe.ucsc.edu. All messages sent to that address are
archived on a publicly-accessible Google Groups forum. If your question
includes sensitive data, you may send it instead to
genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group