ASV collaps question

Hi
Collaps to genus level in qiime2.
It is divided into one with and without a level name.
Can’t you see the same bacteria?

Thank you.%EC%BA%A1%EC%B2%98

1 Like

@shinseung,
Those two labels are distinct:

  1. The first indicates that the sequence could not be classified beyond kingdom level (which probably indicates that it is really non-bacterial, e.g., host DNA).
  2. The second consists entirely of labels from the reference database you used. So QIIME is able to classify that sequence to the genus (or species?) level, but unfortunately the top match is to reference sequence(s) that are totally unannotated in the database.

I hope that clarifies!

3 Likes

Thank you for answer.
I don’t have the same species level name, so I wonder why it’s different. What’s the difference between the two bacteria?

  1. The first indicates that the sequence could not be classified beyond order level. Collapsing at species level causes QIIME 2 to fill in empty levels with “__” to indicate that no label is present at that level.
  2. The second QIIME was able to classify that sequence to the species level, but unfortunately the top match is to reference sequence(s) that are only annotated to order level in the database.
1 Like