QIIME

Quick Reference for running QIIME on Amazon AWS

 

QIIME 1.7.0 (release) AMI:
ami-9bc9a7f2

To mount an EBS volume:

mkdir ~/data
sudo mount /dev/xvdf ~/data
sudo chown ubuntu ~/data
sudo chgrp ubuntu ~/data


 

Quick Guide to Common Commands

Assigning Taxonomy to 18S sequences via RDP:

parallel_assign_taxonomy_rdp.py -i /Users/hol
lybik/Downloads/Clustered_OTUdata/QIIME/Uclust99_PrimerF04andNF1/OTUrepset_uclu
st99_F04NF1.fasta -o /Users/hollybik/Downloads/Clustered_OTUdata/QIIME/Uclust99
_PrimerF04andNF1/rdp_assigned_tax_30Apr14 -T --jobs_to_start 2 --reference_seqs
_fp /macqiime/silva_111/eukaryotes_only/rep_set_euks/99_Silva_111_rep_set_euk.f
asta --id_to_taxonomy_fp /macqiime/silva_111/eukaryotes_only/taxonomy_euks/99_S
ilva_111_taxa_map_RDP_7_levels_euks.txt --confidence 0.7

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: