I'm looking to use either Bowtie2 or GMAP/GSNAP to try to map sequences to gene names. The FASTA file that I want to index contains all of the genes from a species. Problem is, I keep getting errors when I try to index this FASTA file, as GMAP wants a chromosomal assembly I believe. The problem with using the chromosome assembly as an index, is it won't tell me what that gene is (hence why I create my own FASTA with gene names.) Does anybody have any suggestions for this?