creating taxa summary using RDP classifier

[zilberm...@gmail.com]

I am trying to use the RDP classifier to assign taxonomy to a fastq files. I used assign_taxonomy.py -m rdp ....

This worked and we get an output file of this format:

B11_1846119 k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales 1.000

B11_920149 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Trabulsiella;s__farmeri 0.950

H11_2163595 k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__S24-7;g__;s__ 1.000

E11_2727411 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae 1.000

D11_126027 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Trabulsiella;s__farmeri 0.950

H11_2133877 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae 1.000

E10_1178442 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae 1.000

E11_2096990 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae 1.000

C11_2100975 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Trabulsiella;s__farmeri 0.970

H10_2532204 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae 1.000

G10_122109 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterial

I now want to get a relative abundance output (as I get from the summarize_taxa.py script). How can this be achieved. 

Any advice will be appreciated.

[justink]

take a look at adding that taxonomic data to your OTU table with

make_otu_table.py

then looking at the taxonomic data with e.g.:

summarize_taxa_through_plots.py

Best!

-justin

[Meirav Pevsner Fischer]

To run the make_otu_table.py  created a otu_map.txt with the script: pick_otu.py.

I ran the default script but then after taxa summary it gave me taxa assignment: non;other;other  for all samples

any advice?

Thanks a lot

Meirav

[justink]

if they're all "non;other;other", I suspect there's an issue with the command. Would you paste the first few lines of each of your input files to assign_taxonomy.py and the exact command you typed into the terminal?

thanks.