Hello all, I was working on an analysis using Kraken with the Standard_PlusPF database, but I have been observing some strange things in my results. In the relative abundance in Bracken, kingdoms such as Bacteria and Archaea appear, as you can see in the file I will share with you. It's strange, isn't it? Since this is an ITS analysis using databases only for fungi and protozoa. I believe it might be because I am using data related to ITS regions in shotgun databases. Sorry if I might be making a mistake by performing ITS amplicon analysis with a shotgun database, as I didn't see anywhere stating that this wasn't possible. Additionally, I am new to the field of bioinformatics.
I would also like to ask if it is possible to use 16S region data with shotgun databases. I noticed that for 16S regions, the Standard-16 database didn't show much difference when compared to GG. However, when I run it with the Standard database, some eukaryotic data also appear.
Hello all, I was working on an analysis using Kraken with the Standard_PlusPF database, but I have been observing some strange things in my results. In the relative abundance in Bracken, kingdoms such as Bacteria and Archaea appear, as you can see in the file I will share with you. It's strange, isn't it? Since this is an ITS analysis using databases only for fungi and protozoa. I believe it might be because I am using data related to ITS regions in shotgun databases. Sorry if I might be making a mistake by performing ITS amplicon analysis with a shotgun database, as I didn't see anywhere stating that this wasn't possible. Additionally, I am new to the field of bioinformatics.
I would also like to ask if it is possible to use 16S region data with shotgun databases. I noticed that for 16S regions, the Standard-16 database didn't show much difference when compared to GG. However, when I run it with the Standard database, some eukaryotic data also appear.
BEN-ITS.bracken.txt