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
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
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