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
Here is an [illustration of differences][1] between CDS/transcripts. 

You can find cDNA's and CDS's for *Felis catus* [here][2].

Ideally you should align your data to the genome and then use an annotation file to do counting of reads.

Added: If you are using `salmon` then you should use transcripts.

  [1]: https://biology.stackexchange.com/questions/11377/difference-between-cds-and-cdna
  [2]: ftp://ftp.ensembl.org/pub/release-92/fasta/felis_catus/