search

joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
582 stars 187 forks source link

Aggregated phlylogenetic tree #397

Closed JB-8 closed 8 years ago

JB-8 commented 9 years ago

Hi,

I have a dataset which I aggregated to the Class level using "tax_glom(master,taxrank=Class)". If I understand the function correctly, all OTUs which belong to the same class are grouped together.

I was wondering what actually happens to the phylogenetic tree in this step. The see is also trimmed to contain only the classes, but how is this step performed? How are OTUs from the same class arranged in the new tree?

The same question is also valid for other function such as selecting only the Top 100 OTUs.

Thanks for your reply, Julia

ByronBa commented 9 years ago

Hi Julia,

Sorry that I am posting something not related to your post! I have encountered the same problem as you had before. https://github.com/joey711/phyloseq/issues/349#issuecomment-61280709 Could you please tell me how you solved the problem? Thank you very very much!!!

Byron

JB-8 commented 9 years ago

Dear Byron,

I got it working after re-running the .biom conversion to .txt of my OTU table. I created my OTU table in .biom format in QIIME and then converted it to a text file before importing it into phyloseq. Are you doing it the same were or are you running a different pipeline?

Try using the following command and then import your files into phyloseq again:

biom convert -i otu_table.biom -o otu_table.txt -b --header-key taxonomy --output-metadata-id "Consensus Lineage"

Before the update, the metadata-id was just "Lineage". For me it did not work to simply change the header in Excel, but after re-running this conversion I was able to import the files smoothly into phyloseq.

Best, Julia

JB-8 commented 9 years ago

I guess these comments should go to issue #349 - could you move them to the right place?