18S workflow with Illumina sequences

[Laura]

Hi everyone!

This is my first message to this helpful forum. I think it’s wonderful that we can share our knowledge about QIIME :).  I hope my question is not repeated, although I haven’t found it. 

I have sequences from the Illumina MiSeq system. These are 18S sequences. What I have done so far is:

1. Create and validate the mapping file (No errors or warnings found)

2. Generate a single archive containing all sequences (add_qiime_labels.py) 

In this step, what I want to do is to generate the OTU  table and assign taxonomy. (What I do with 16S bacterial data is using the script pick_open_reference_otus.py with –r 97_otus.fasta, from greengenes, and with this I obtain the taxonomy data I need).

I want to generate the OTU table and assign taxonomy to my 18S sequences. I have downloaded the Silva 119 release, which has a 18S database. 

Which scripts should I follow to assign taxonomy to these 18S sequences?

I’ve been looking at pick_otus.py but I don’t know if it’s the correct script and which parameters should I use.

Thank you in advance to you all!

Laura

[Colin Brislawn]

Hello Laura,

The scripts pick_otus.py should be a good fit for your data. pick_open_reference_otus.py is also a good fit. 

I think the ITS tutorial would be a very good starting point, because it also has to use non-default databases. 

http://nbviewer.jupyter.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/Fungal-ITS-analysis.ipynb 

Let me know if that tutorial helps, and let me know if you have any other questions.

Colin