[galaxy-user] Reference genome , fasta with or without gene feature

Dear All I am analysing bacterial RNA seq (illumina). as my reference genome is not in galaxy. so i need to downlaoded the reference genome from  NCBI and upload to my history Should i use reference genome with  gene features or  single  fasta file with out any annotation information. even after download should i need to modify or it should be used as it is. Thanks in advance Ateeq