I am running into some weird questions when I am doing fungi taxonomy work with Illumina result on Qiime 2.
Fungi gene were sequenced on ITS1and 2 primer on Illumina platform. The result came back like this.
I thought it could be a wrong choice for ITS gene database (I used SILVA full dataset include ITS genes and matched to UNITE taxonomy)
But when I decided to extract all the entries and relative frequencies of each entry, the abundance does not match.
This is ranked from highest abundance to lowest.
Apparently, the first entry (~25%) does not match the high abundance from the taxonomy (~50%).
I BLASTed each single entried and it returns with mostly Kazachstania sp.
I am having a hard time figuring out where I had done wrong.
Could Qiime combine entries it cannot classify into one big entry and show in the taxonomy bar plot?
What can I do to trouble shoot?
Thanks a lot!
If anything does not make sense, I can add more information on!
Hello!
Looks like you are comparing ASVs and taxonomy annotations!
But, in fact, each ASV is assigned to certain taxa (or unassigned at all), meanwhile to each taxa numerous ASVs may be assigned. So, each taxa in the barplot is a sum of all ASVs assigned to it.
It is why ASVs relative abundances do not identical to the barplot.
Hope I understood your question correctly.
First time encountering this taxa Kazachstania sp.
Hello!
This is exactly what I wanted to know! I was not sure whether having multiple ASVs to be assigned to the same taxonomy in the bar plot is possible.
If this is the case for me, is there a way to find out which ASVs were assigned to say the highest abundant taxa?
Hello!
You schould already have an artifact called something like 'taxonomy.qza', which you can either visualize or import to a tsv file. This file will show taxonomy annotation of each ASV, so you can just perform a search by certain taxa and get all ASVs assigned to it.
Hi Timur!
I did not notice that I had that already. I must have overlooked at it.
Thanks for the reminder! Seems to be much easier to solve than I thought.
