Announcement

Collapse
No announcement yet.

Taxonomy tree conflicts in Greengenes V 13.5

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • uloeber
    replied
    Thank you!

    Leave a comment:


  • asorbie
    replied
    I think they may have changed some minor things this year but not the entire database. 13-5 is the May 2013 release.

    Leave a comment:


  • uloeber
    replied
    Really? I used version 13-5 released this year 2019-05-01

    Leave a comment:


  • asorbie
    replied
    Greengenes hasn't actually been updated since 2013. Personally, I just wouldn't use it at all. Stick to Silva, RDP or GTDB if possible.

    Leave a comment:


  • uloeber
    started a topic Taxonomy tree conflicts in Greengenes V 13.5

    Taxonomy tree conflicts in Greengenes V 13.5

    Hi all,
    I'm using the Lotus pipeline to investigate 16S stool samples. I assigned taxonomy with Greengenes, SILVA, HITdb , since greengenes was updated most recently, SILVA is the biggest database and the unassigned OTUs could then be classified by HITdb.
    I was not surprised, that tree conflicts occurred, but what was surprising was that greengenes itself (V 13.5 05/2019) included conflicting information, or how would you judge this:
    158718 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__

    186714 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__[Paraprevotellaceae]; g__[Prevotella]; s__

    What does the parenthesis mean? Anyways, unfortunately, this results in one genus on different nodes, retrieved from one database!

    Looking much forward for a fruitful discussion with you.

    Cheers,
    Ulrike
Working...
X