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WrightonLabCSU / DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
GNU General Public License v3.0
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"Present in contig" in dramv distill product heatmap #253

Open ereyred opened 1 year ago

ereyred commented 1 year ago

Hello! What does "present in contig: true/false" mean in the heatmap? Only a few contigs are labelled as "true" for named vMAG functions (6 out of 45). Does this mean the rest have not been successfully identified/annotated? If so, is this ratio of annotation normal? What can be done to improve it? Thanks so much.

jrr-microbio commented 1 year ago

Hey there,

Thanks for using DRAM-v!

In the product.html heatmap, the "Present in contig: True/False" refer to whether the specific gene (each square) is present or not in the viral contig. The heatmap that is being generated is based off of the categories from the DRAM bacterial/archaeal heatmap that shows different microbial metabolisms, and so this heatmap is more appropriately interpreted as "potential AMGs" encoded in your vMAGs. Note that there are no viral-like genes or categories here, just metabolisms. As such, 6 of 45 possibilities is reasonable, as we would not expect a virus to be able to perform all of these metabolic functions.

I would recommend checking your amg_summary.tsv file for more details as to what genes are present / getting called as a putative AMG and use the flags / auxiliary scores to manually assess these.