Question: Tool to estemate Ka/Ks using variant calling data?
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gravatar for wbrutter
4.4 years ago by
wbrutter0
United States
wbrutter0 wrote:

Hi,

I'm in the process of comparing RNA-seq data from two fungal isolates by aligning against a refrance of the same species.  I've performed the alignments using Tophat, and called variants using the GATK haplotype caller. I'd now like to estemate the Ka/Ks ratio for all the genes in my referance. However, the only programs I can find to calculate this require Fasta alignments. could anyone recomend a software or pipline that would get me what I need? I'd appriciate any advice.

Thanks

snp rna-seq • 1.5k views
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