Hi,
It is possible to download bulk data from UCSC using user-friendly tables, however, this recipe appears to be restricted to a single species. BioMart is similar in this respect allowing you to explore data once a species is identified. (Comparative analysis is also understandably restricted to few species at a time.)
Is it possible or there an easy way (e.g., through Galaxy or without having to use API) to download sequence or sequence features in batch for many species?
Such data collection exercise has recently become a routine and I would be happy to know if there is a trick that I might have missed.
An example would be to download all 5' UTR sequences for a given list of transcript ids from a number of species at various phylogenetic depth (clearly, whenever available).
Thank you
Check Ucsc Genome Browser Automation: Command Line Scripting. and Is There Such A Thing As A Ucsc Api?