Thanks for your help!
I’ve now tried using both the gencode and UCSC fasta hg38 transcriptomes you’ve provided links to but unfortunately I’m still getting errors when it runs (this is occurring with both the directly downloaded and unzipped files and the files I ran through ‘NormaliseFasta’ first). I’ve also removed the GTF headers according to the FAQ link provided and tried running Salmon both with and without.
The error report it’s giving me back is similar but looks a little different now (see below).
Is it possible that the problem is with the RNA STAR BAM files I’m trying to put through salmon? They were aligned to the inbuilt HG38 reference genome but without a GTF. I’m only thinking this since on the error report it repeatedly says ‘warning transcript XXXXX appears in the reference but not the BAM’.