Hi all, I prepare to download annotation file(gtf) from ucsc to do rna-seq analysis, but i can not download directly. So i preapare to download mouse txt file and use genePredToGtf to transfer it to gtf file. I have a question, the table browser page has "track:" ,it has different choice. like ucsc genes sgp genes and so on. which one should i choose? Thanks!
Tracks are different annotations that can be added to your view in the UCSC genome browser; so it's really up to you which one to choose. They are aligned to the genome and can be either computed by UCSC or provided by others.
Do you want the ab initio prediction only? Then, choose AUGUSTUS. Are you interested in a set of annotations of the coding genome that is an agreement between several resources? Then choose CCDS. And so on so forth.
Selecting the "output format" as GTF and then hitting "get output" works for me: