Hi, 

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
You should not map against the genome using Salmon.  You can either download a transcriptome file, or a genome file and transcript annotations, and use a tool like gffread to extract the transcript sequences.  You most likely want to quantify against the cDNA to account for features such as UTRs.