Hi,
I am trying to use Decontam to clean my data. This is my first time using it and I am running into an issue with my taxonomy table. When uploading my taxa table and taxonomy into R I am using the following script and this is working find:
However the taxa count is only 4 in my OTU table and I get this result:
phyloseq-class experiment-level object
otu_table() OTU Table: [ 4 taxa and 59 samples ]
tax_table() Taxonomy Table: [ 4 taxa by 7 taxonomic ranks ]
The issue is that when I use the exact same table_lily2.qza to create a bar plot I can clearly see that there are way more than 4 taxa, so I do not know what the issue is. I tried to look up why this may be happening but I am not finding any resources.
Hi @liliez13 I am unsure about why your taxonomies are different, but from my understanding you are trying to upload a qiime obj into R as a phyloseq obj to use Decontam correct? If so you can sidestep this by using the latest Qiime distribution to run Decontam processes as the functionality is integrated into the quality-control plugin
Hi,
I only have two controls so I am unable to use the qiime distributionto run Decontam since it requires a minimum of 5 control samples.
Do you have another suggestion on why this may be occuring?
Ah I see, it was initially implemented in that way as the recommended number of control samples is 5, however in later distributions this requirement was removed, in favor of a warning message. Which Qiime distribution are you using?
You see more info about control requirements for decontam here.
That is the first distribution of Qiime to use decontam so it has the initial implementation that has the requirement of 5 control samples. All you have to do is upgrade your qiime2 distribution to the latest and you shouldn't have a problem!