Regarding --all_results option

[ShailNair]

Hi,
Thanks for the pipeline. It made my work easy. I am interested in identifying iron siderophore synthesis in my metagenomic samples. When I run the fegenie pipeline without --all_results the output heatmap.csv shows iron_aquisition-siderophore_synthesis as 0,0,0,0,0.
if I include --all_results tag in my command it shows as iron_aquisition-siderophore_synthesis,2592,2488,5138,5511,1979.
It is very strange to get 0 counts considering my samples are from a natural environment and consist of a diverse bacterial community.

What's the difference between the above two commands (with and without --all_results tag)?
The help section says --all_results: report all results, regardless of clustering patterns and operon structure

I didn't clearly understand what does that actually means.

Does it have anything to do with search accuracy?

[Arkadiy-Garber]

Hi there! Thanks for your interest in FeGenie. siderophore synthesis operons are quite tricky to identify. Lots of genes that are part of these pathways appear to also be part of other pathways. So, we implemented fairly strict guidelines for reporting possible siderophore synthesis operons. This is likely why you are not seeing any hits when you run the pipeline without the --all_results flag. With that flag, you get a lot more hits, but it is likely that many of those hits are false positives. Does that make sense? We are currently working on an updated version of the software that performs better at identifying siderophore synthesis operons.

Not sure if you are familiar with AntiSMASH, but that is another software that specializes in biosynthesis gene clusters, including siderophore biosynthesis operons. I would recommend you try that out. It is available as a standalone command-line tool, and also as an easy-to-use web server, available here: https://antismash.secondarymetabolites.org/#!/start.

Hope this helps! Let me know if you have any questions!

Thanks,
Arkadiy

[ShailNair]

@Arkadiy-Garber Thanks for the explanation. I did check with AntiSMASH. but did not get much luck. there a few hits with a poor similarity percentage. Can we expect Fegenie update sooner (I know it takes a lot of time and testing to release even a minor update and I respect that the package developers are working hard).