taxonomy assignation

[Muriel]

Hello,

 

I have a question on the taxonomy generated after Summarize Communities by Taxonomic Composition.

 

What is the difference with the 2 taxonomy below that were both in the same file? Why is one line with "Other ; other) and one with "f _ g".

 

 

Root;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales;Other;Other
Root;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales;f__;g__

 

Kind regards,

 

Muriel

[Tony Walters]

Hello Muriel, 

The "Other" assignments are due to ambiguity when the RDP classifier tries to assign below the order level in this case (can't decide between distinct taxa). The f__;g__ means that it did match a reference sequence well, but that reference sequence is poorly defined (not named at family level or lower).

Hope this helps,

Tony

 

Muriel

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[Muriel]

Hi Tony,

 

thanks for the reply. I take the opportunity also to ask you how it is possible to split the headers of the columns at the different levels of taxonomy. My problem is when I open the level 6 file in excel, all the taxonomy is within a header row.

For example to show split at each underscore between eg: root_actinobacteria;c_actinobacteria;o_etc into columns with header: root actionbacteria_c actinobacterio_o

 

thanks,

 

Muriel

[Tony Walters]

Hello Muriel,

You probably want to split on semicolons, as those are separating the taxonomic levels.  See this thread about splitting with Excel (http://www.mrexcel.com/forum/excel-questions/416510-split-data-after-each-semicolon.html)

-Tony

[Muriel]

Hi Tony,

 

yes it owrked in excel in "data" then "convert".

 

Thanks,

 

Muriel

[Muriel]

Dear Tony,

 

I come back to you again concerning the file "level 6"=genus generated after "taxa summary". I realized that for some genera (Clostridium, Ruminococcus", I do have several lines with the same taxonomy. For example for Clostridium I do have 4 times this line, and in each line, I have relative abundance >0%.

 

Root;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Clostridium

 

 

 Is it correct to add the relative abundance of each line into the genus "Clostridium" or did something go wrong with the database? I used greengenes.

[Muriel]

just an extra information. Actually the 4 lines with Clostridium genus have different families.

 

Root;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium

Root;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Clostridium

Root;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Clostridium

Root;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium Is it correct to sum the % of abundance of each into genus "Clostridium"?   Muriel

[Tony Walters]

Hello Muriel,

I wouldn't sum them in this case-you want the taxonomy string to completely match before summing (some of the older taxonomic naming conventions based on morphology/biochemistry don't always match with phylogeny, as you can see here).

-Tony