I was trying to create an index for salmon tool (v 1.0), using the following command:
salmon index -t gencode.v33.transcripts.fa -i index_salmon_v33
It seems to work but gives a warning:
[puff::index::jointLog] [warning] It appears that this may be a GENCODE transcriptome (from analyzing the separators in the FASTA header). However, you have not set '|' as a header separator. If this is a GENCODE transcriptome, consider passing --gencode to the pufferfish index command.
Hence, I started wondering if it is normal at all to use gencode transcriptome, or it's not the default recommended way? I found that this warning comes not from salmon itself but from pufferfish module - but I don't know if it's important, or I should just ignore it.