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snayfach / MIDAS

An integrated pipeline for estimating strain-level genomic variation from metagenomic data
http://dx.doi.org/10.1101/gr.201863.115
GNU General Public License v3.0
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non-synonymous sites #87

Closed palomo11 closed 6 years ago

palomo11 commented 6 years ago

Hi,

I have a doubt when using snp_diversity.py. I want to quantify diversity at non-synonymous sites, based on the example in the tutorial:

snp_diversity.py /path/to/snps --genomic_type genome-wide --sample_type pooled-samples --site_type 4D --locus_type CDS --out /path/to/output

I should use --site_type 4D, but in the description of the different option it says:

--site_type {1D,2D,3D,4D}
if locus_type == 'CDS', use genomic sites with specified degeneracy: 4D indicates synonymous and 1D non-synonymous sites

So to quantify diversity at non-synonymous sites, should it be use --site_type 4D or 1D?

snayfach commented 6 years ago

Good catch. Use 1D for non-syn and 4D for syn. I've updated the documentation

palomo11 commented 6 years ago

OK, thanks.

By the way if I have several species across several samples is there any way to calculate the dN/dS using MIDAS?

Thanks in advance!

snayfach commented 6 years ago

No there's not, sorry

On Mon, Jul 9, 2018 at 12:19 PM, palomo11 notifications@github.com wrote:

OK, thanks.

By the way if I have several species across several samples is there any way to calculate the dN/dS using MIDAS?

Thanks in advance!

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