FeGenie
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Arkadiy-Garber
HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes
Awesome product! Many problems mentioned in the issues could be solved by rewriting the workflow using a proper manager. This would also properly parallelize tasks. Best
Hey! I do have another question! After annotating my MAGs, I saw that FeGenie didn't find any transport-related clusters in any of my MAGs, which wouldn't make sense biologically (I...
After running FeGenie with a reference database (nr.dmnd) I get the error shown below. As an output I get the complete FeGenie-summary.csv and an empty file FeGenie-summary-altered.csv. I think I...
Hi there, and thank you for this tool! I am trying to run some metagenomes through FeGenie and have been successful so far, but I am trying to understand the...
Dear Arkadiy Garber, I just watched your FeGenie lesson and tutorial in the BVCN and, first of all, I wanted to thank you for the nice tool (and teaching materials)...
Hi, Thanks for the tool. Since I found that the annotations obtained from FeGenie installed by conda were few. I test the FeGenie installed by conda and the FeGenie installed...
Hi, I would like to create conda package for FeGenie. In order to do this, having a license file that allows distribution in the repo is required, and having official...
Hi, I'm interested in identifying iron related genes within a metatranscriptomics dataset. I have attempted providing a fasta with gene (nucleotide) or protein sequences as bellow, but I hit an...
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**...
Hello Arkadiy, --norm, if include this flag, the gene counts for each iron gene category to be normalized to the number of predicted ORFs in each genome or metagenome. Without...
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HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes