I have one query regarding Taxonomy analysis. If I add my desired sequence along with my Greengene database, its not picking my desired sequence in taxanomy analysis. but if i run desired sequence alone mean sequence was Picked up.
For instance, Moraxella; s__osloensis was not seen in sample 2 if i perform taxonomy analysis with greengene database along with desired sequence. it was seen in sample 2 if i perform analysis with desired sequence.
Could anyone tell me how to rectify this error? Herewith, I have attached result and sequence file for your perusal.
First, I’ve moved this user support because it’s not a technical problem.
First, how did you assign your taxonomy? Did you train a feature classifier? Did you use vsearch or blast or something else? Your overall rate of unassigned sequences seems quite high to me, so that’s a bit concerning.
Second, depending on your method, it’s possible that only a few sequences hit your target of interest in the filtered database. What classification method did you use there? What is the confidence on those assignments comopared to the confidence on the greengenes assignment? Have you filtered the greengenes table to check if your sequence of interest appears there and at what relative abundance? What if you blast the representative sequences against your reference?
