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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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question about pangenomics workflow anvi-summarize gene clusters #921

Closed Alopias1988 closed 6 years ago

Alopias1988 commented 6 years ago

Hi,

I have a question about the structure of the file when you run the anvi-summarize command resulting in a file with the annotation of the gene clusters of all genomes. In the gene function column it shows functions separated by a "|", I think these are function of the genes in the cluster? I am asking because when I compare it with the matrix with the presence/absence of functions not all the functions present in the summary file are also in the matrix presence/absence one. Is it because its only taking the first function and disregarding the following ones separated by "|". Sorry if this is obvious or explained elsewhere, but I couldn't find explanation

Thanks!

ShaiberAlon commented 6 years ago

Hi @Alopias1988,

I think this includes the explanation your are looking for (copied from http://merenlab.org/2016/11/08/pangenomics-v2/#making-some-sense-of-functions-in-your-pangenome). I highlighted the most relevant part:

image

Let me know if you have any more questions please.