I have non-model plant transcriptome data that has to be assembled in reference based mode. Now my question is to what would be best choice as reference : cDNA or CDS
Now as I understand cDNA sequences are the transcript sequences from a gene while CDS sequences are parts of cDNA sequence (or exons). right ?? So will mapping to CDS suppose to guide the assembler better ???
PS: both cDNA and CDS is draft mode even the genome. And it has to be cDNA or CDS, cannot map it to the genome.