I had issues in the past trying to use mouse or human FASTA and GTF from Ensembl or UCSC. After many frustrated attempts I solved it using links from GENECODE that work just fine.
I am now trying to analyze some RNAseq from Danio rerio (zebrafish) and run into the same issue with the exception that i cannot take the GENCODE shortcut.
Can someone provide me the links for the reference genome and gene model for zebrafish to fetch the data?
thanks