Does anyone know what is the best way to download the ENSEMBL and REFSEQ canonical transcripts for HG38? Any suggestions would be greatly appreciated!
For RefSeq data, use the tool "Get Data: UCSC Main".
For ENSEMBL data, either extract from UCSC as above, or use the tool "Get Data: Biomart".
Both external data providers have help for usage (see their web forms) and when accessed from within Galaxy, will return results to your active Galaxy history by default.
What's the difference between a genome nd a canonical genome?
When choosing a reference genome, what's the difference, e.g. between hg38 and hg38 canonical?