Using RDPTools to assign taxonomy

RDPTools comes across as a pretty useful way to assign taxonomy if you are having some trouble with the greengenes database.

I was having some trouble working with the database because I was unable to find mappings that were unique for the 16s sequences I had.

It looked like there might be multiple different 100 percent matches to the greengenes database.

After confirming that sometimes these matches were for different bacteria. I was starting to doubt whether I was using the database effectively or even correctly so I decided to check with another database tool. Hopefully this would tell me whether there was a problem with my sequences or I needed to change the way that I was using greengenes. I considered that possibly I should make a database of my 16s and see what greengenes sequences matched.

RDP has most of their information available on their github at: This location Once you have finished installing and combined the 16s rRna that you need to look at into one large fasta file all that you need to run is

java -Xmx1g -jar /path/to/classifier.jar

to get the help options

to classify your samples and output a csv file you run

java -Xmx1g -jar /path/to/classifier/jar -o /path/to/output.txt /path/to/fastaInputFile.fasta

This will take in your fastaInputFile.fasta and spit out an output.txt file in the location yous pecify.