hello,
I am looking for some virulence factors in aeromonas genomes. I use abricate and VFDB yet I can’t find what I need (I know the genes are present as the samples are PCR positive and I also found them in the asseblate using blast). I don’t understand why I can’t find them with abricate (this is one of the genes in question VFDB - aerA/act gene (VFG038892)). I also tried using abricate with a reference genome that I know for a fact contains the gene. I thought that maybe it was not present in VFDB but in the publications it is used without problem for those genes.
Have you tried to visualize the assembly and annotation in a genome browser? IGV would be a good choice for this.
Some of these tutorials are still in development (we are working to incorporate IGV directly into Galaxy) but you can use it as a stand-alone application from your own computer, and load files through Galaxy if the database (genome) metadata is set up. Or, download the files and upload directly. I also added a tag to this topic that will link to prior topics with how-to-use help.
