I am trying to find a definitive answer to my problem: shall I use annotation file to make a genome index or not? In a bioinformatics workshop I attended the instructor said there is no fall out of not using the annotation file while making the index. I am aware that hisat2 website provides pre-built indices. However, I want to use gencode annotation files or lncipedia files which are not suitable for hisat2 provided indices.
I found a similar unanswered question on seqanswers
Any suggestion is highly appreciated!