estimation of non synonymous over synonymous (Ka/Ks) SNPs over genome with RNAseq

[piemmea]

dear all
I performed RNAseq in closely related plant species and was asked to perform a Ka/Ks estimation of the transcriptome. The problem is, that a number of genes are not fully covered, so I was wondering just to consider just those who are 100% covered. However, in some papers it seems that people look at single codons, not whole CDS, so the question is: do I consider the first option or the second is correct as well? Clearly, if I would consider also genes with incomplete coverage, I could get higher numbers. In case, does anyone can suggest me a software?
Many thanks
Marco

[upendra_35]

I don't know if it is too late for you but i recently did something in the lines that you mentioned above - using RNA-Seq data to calculate Ka/Ks ratio for two genomes. For this first i have reconstructed the genomes of these species by incorporating the SNPs and then used KaKs calculator (https://code.google.com/p/kaks-calculator/) to calculate Ka/Ks ratio. Let me know if you need further details. Good luck!

Thanks
Upendra