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Old 12-16-2014, 12:53 AM   #1
fmoejes
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Default Qiime parallel_pick_otus_uclust_ref.py

Good morning everyone!

I ran parallel_pick_otus_uclust_ref.py with a high quality fasta file and silva.nr.v119.align as the refence file.

On the QIIME website it says you should get two files - a .txt and a .log file. However, I got a directory file 'POTU_gdTg_'. And when you open this directory you get several files - deletion_list.txt; expected_out_files.txt; merge_map.tt; POTU_gdTg_.0.fasta; POTU_gdTg_.1.fasta; POTU_gdTg_.2.fasta; POTU_gdTg_.3.fasta; POTU_gdTg_.4.fasta; POTU_gdTg_.5.fasta; POTU_gdTg_jobs.txt.

Does anyone what these files mean? And which would I use to make the OTU tables? Is there another set before I can create the OTU tables? Do I need to assign taxonomy first?

Thaaaaaanks!!!!
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Old 12-16-2014, 04:45 AM   #2
sfranzenburg
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Are you sure this command is still valid?
Usually, the Qiime OTU tables are in .biom file format since ~2 years.
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Old 12-16-2014, 05:06 AM   #3
fmoejes
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Thank you for your reply!

Yes - the output of make_otu_table.py is a .biom file. But I don't have the tables - that is what I want to do now!

I am wondering what file would be the input file for the make_otu_table.py command?
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