Gathering OTUs

[Caroline Marden]

I don't know if there is a way to do this.

My data set includes a list of OTUs and quite a lot of them are the same thing, like Pseudomonas. When I create a network or a heatmap all the OTUs are listed with many the same genus, so it shows more diversity than there really is. Is there a way to gather OTUs together so I have a sequence count for Pseudomonas? The way I am doing it is to open up the OTU table and manually do it but it is taking ages.

Thanks anyone who can help

Caroline

[Colin Brislawn]

Hello Caroline,

Is there a way to gather OTUs together so I have a sequence count for Pseudomonas? 

Yes! Take a look at this script.

http://qiime.org/scripts/summarize_taxa.html

Colin

[Caroline Marden]

Thanks, yes I have that, I get an excel sheet with L2, another sheet at L3 etc. For instance I want everything found, for instance Proteobacteria unclassifed and bacteriodetes unclassified will not feature in further excel sheets. So the only way I can get everything together is to take everything from each sheet and manually put it together in one sheet to represent everything, convert it to a txt file, then make a new biom file from that? 

Caroline

[Colin Brislawn]

Hello Caroline,

There should be an easier way to do this... Are you trying to merge the different Proteobacteria, or to filter out the unclassified ones? The summarize_taxa script makes all these .biom tables of merged taxa for you.

Perhaps you could use one of those .biom tables as the input to filter_taxa_from_otu_table.py, setting it to remove the unidentified OTUs. 

http://qiime.org/scripts/filter_taxa_from_otu_table.html 

Colin

[divyapr...@gmail.com]

Hi colin 

Will u please elaborate the command as i am getting error. while running the command 

as my biom.table is in Soil_otus/otu_table.biom.

  Please enter the full command so that i can get it.

qiime@qiime-VirtualBox:~$ summarize_taxa.py - i Soil_otus/otu_table.biom -o Summarize-taxa

Usage: summarize_taxa.py [options] {-i/--otu_table_fp OTU_TABLE_FP}

[] indicates optional input (order unimportant)

{} indicates required input (order unimportant)

The summarize_taxa.py script provides summary information of the representation of taxonomic groups within each sample. It takes an OTU table that contains taxonomic information as input. The taxonomic level for which the summary information is provided is designated with the -L option. The meaning of this level will depend on the format of the taxon strings that are returned from the taxonomy assignment step. The taxonomy strings that are most useful are those that standardize the taxonomic level with the depth in the taxonomic strings. For instance, for the RDP classifier taxonomy, Level 2 = Domain (e.g. Bacteria), 3 = Phylum (e.g. Firmicutes), 4 = Class (e.g. Clostridia), 5 = Order (e.g. Clostridiales), 6 = Family (e.g. Clostridiaceae), and 7 = Genus (e.g. Clostridium). By default, the relative abundance of each taxonomic group will be reported, but the raw counts can be returned if -a is passed.

By default, taxa summary tables will be output in both classic (tab-separated) and BIOM formats. The BIOM-formatted taxa summary tables can be used as input to other QIIME scripts that accept BIOM files.

Example usage: 

Print help message and exit

 summarize_taxa.py -h

Examples: Summarize taxa based at taxonomic levels 2, 3, 4, 5, and 6, and write resulting taxa tables to the directory "./tax"

 summarize_taxa.py -i otu_table.biom -o ./tax

Examples: Summarize taxa based at taxonomic levels 2, 3, 4, 5, and 6, and write resulting mapping files to the directory "./tax"

 summarize_taxa.py -i otu_table.biom -o tax_mapping/ -m Fasting_Map.txt

summarize_taxa.py: error: Positional argument detected: -

 Be sure all parameters are identified by their option name.

 (e.g.: include the '-i' in '-i INPUT_DIR')