discrepancies in gene-luster summary from pangenome database and gene-calls from contigs database

[Mir Alvee Ahmed]

Hi,

I'm working with anvi'o v7. I have some MAGs and some downloaded genomes. I followed the pangenome tutorial. Now, to see the differential gene expressions, I was trying to match the gene caller IDs which I got from gene cluster summary of the pangenome with gene caller IDs which were gotten from the contigs database using the anvi-export-gene-calls command.

These two files aren't matching regarding the unique gene caller IDs. Some of the gene caller IDs are missing in the gene cluster summary file and for this, I cannot match all the genes from the contigs database to find out the KEGG or COG information.

Is there a way to fix this? I'm not sure why I'm missing some of the gene caller IDs in this case.

Thanks for any help,

Alvee

[A. Murat Eren (Meren)]

Very interesting. This is the second time I'm hearing this today. Can you please send the exact commands you're using for any of these steps? From creation of the pangenome to exporting the gene calls?

--
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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