If I want to display some data on the UCSC genome browser, but have done the analysis with the Ensembl or NCBI assemblies and annotations, do I need to manually write scripts to replace all the chromosome IDs with the UCSC genome browser ones? It seems like this would be a very common situation that has an existing solution.
Alternatively, I could do my analyses from now on using the UCSC assembly and annotation files, but that seems to have some issues. The annotation is only distributed as a SQL database. I have looked at using the Table Browser in UCSC to get a GTF file, which is what most tools use, but the GTF files I can get have a lot of missing information. They only contain stop_codon, start_codon, exon, and CDS elements. Can I get it to have transcript and gene entries also? It also only gives the gene and transcript IDs, whereas the GTF files you can get from Ensembl or NCBI have a lot of useful information such as gene symbol and biotype.
I think I might be missing something because it seems like I'm having to jump through a lot of hoops for something that I suspect a huge number of people have dealt with before.