I’ve tried to align RNA-seq reads to a custom genome but I cannot see any alignment. Could it be that I directly uploaded genomic.fna.gz without decompressing and converting to FASTA format?
If so, how can I accomplish it? When I extract the file from the genomic.fna.gz file, I get an FNA file. Should it be additionally converted to FASTA format and how?
Are some other steps, like indexing, needed with Galaxy tools on the FASTA genome file for the following steps before alignment?