anvi-get-sequences-for-gene-clusters

[Emily St. John]

Hello, 

Just a quick question for you! I'm running anvi-get-sequences-for-gene-clusters on my pangenome, using a list of gene cluster IDs (command: anvi-get-sequences-for-gene-clusters -p pangenome-PAN.db -g GENOMES.db --gene-cluster-ids-file list.txt -o seq.faa). Based on the gene cluster output from anvi-summarize, I expect to recover 32 genes, which I do. However, Anvi'o also gives me the following message: "Your filters resulted in 8 gene clusters that contain a total of 392 genes. for downstream analyses. Just so you know." Can you point me to what these 392 genes may be? 

Thanks so much for your time and help!

Best,

Emily St. John

[Florian Trigodet]

Hello Emily,

It is the total amount of genes in all your genomes after the filters.
For instance, if you had 8 gene clusters for which there was one gene found in each genome and you had 49 genomes: 8x1x49=392 genes.

Hope it clarifies a little bit!
Best,
Florian

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Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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[Emily St. John]

Hi Florian, 

Thanks so much for the clarification!

Best,

Emily

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Emily St. John

Reysenbach Lab