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caporaso-lab / student-microbiome-project

Central repository for data and analysis tools for the StudentMicrobiomeProject.
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Closed Reference OTU Picking - Jon Leff #11

Closed floresg closed 11 years ago

floresg commented 11 years ago

pick_reference_otus_through_otu_table.py -i /scratch/caporaso/student_microbiome/slout_fecal/seqs.fna -o /scratch/leffj/student_microbiome/ucr_fecal/ -r /home/leffj/gg_files/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta -t /home/leffj/gg_files/gg_otus_4feb2011/taxonomies/greengenes_tax.txt -aO 50

pick_reference_otus_through_otu_table.py -i /scratch/caporaso/student_microbiome/slout_tongue/seqs.fna -o /scratch/leffj/student_microbiome/ucr_tongue/ -r /home/leffj/gg_files/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta -t /home/leffj/gg_files/gg_otus_4feb2011/taxonomies/greengenes_tax.txt -aO 50

pick_reference_otus_through_otu_table.py -i /scratch/caporaso/student_microbiome/slout_forehead/seqs.fna -o /scratch/leffj/student_microbiome/ucr_forehead/ -r /home/leffj/gg_files/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta -t /home/leffj/gg_files/gg_otus_4feb2011/taxonomies/greengenes_tax.txt -aO 50

pick_reference_otus_through_otu_table.py -i /scratch/caporaso/student_microbiome/slout_palm/seqs.fna -o /scratch/leffj/student_microbiome/ucr_palm/ -r /home/leffj/gg_files/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta -t /home/leffj/gg_files/gg_otus_4feb2011/taxonomies/greengenes_tax.txt -aO 50

gregcaporaso commented 11 years ago

Did you guys not end up using the data I generated as described here:

https://github.com/gregcaporaso/student-microbiome-project#otu-picking

Just want to know where these fit in.

floresg commented 11 years ago

Yes, we are only using the closed reference otus as described in the above commands. We did not use the open reference otus picked as you (Greg) described.

gregcaporaso commented 11 years ago

OK, I will replace my commands with Jon's and close this issue.