I just had a quick question that I started to confuse myself with. When I am about to index my reference sequence for some RNA-Seq data and I got confused if I use the cDNA or CDS or transcript fasta file.
In the past I used a transcript fasta but I can't seem to find one for the species an am working with from ensembl (http://useast.ensembl.org/info/data/ftp/index.html/)
Maybe I can just use the whole genome for the reference? I am using Salmon to map the reads.
Thanks in advance