Metagenomes (xeno, gom_fungi) and rerunning Open Ref OTUs

Xeno HiSeq data – Talked with David, still trying to figure out if we have xeno in there (David will run the raw reads through PhyloSift). What I’m doing:

  • Running Xeno data through MG-RAST. Trying to get an initial overview of the shotgun data
  • Running Xeno data through QIIME (prefiltering, ref-based picking only at 60%) to pull out any rRNA reads that might be in there. Hopefully we can get a better picture of the microbial community. Command ran:
!pick_closed_reference_otus.py -i /Users/hollybik/Desktop/Data/metagenomes/HB_RN_March2013_XENO_unzip.fasta -r /macqiime/silva_111/rep_set/Silva_111_full_unique.fasta -o /Users/hollybik/Desktop/Data/metagenomes/xeno_qiime60prefilter -p /Users/hollybik/Dropbox/QIIME/qiime_parameters_filterMGforrRNA.txt --parallel -O 2

Also uploaded GOM_Fungi data to MG-RAST to get an idea of what’s in the sample – data is processing through the pipeline now.

Made some final tweaks to the open ref OTU picking protocol on StarCluster. This should hopefully be the final command that will run to completion after changing the SC script in qiime_config:

!pick_open_reference_otus.py -i /gom_data/GOM_concat1.7_rev_demulti_1to12_2.fna -o /gom_data/uclust_openref96_ref_22Aug -r /gom_data/99_Silva_111_rep_set_euk.fasta --parallel -O 8 -s 0.1 -p /gom_data/qiime_parameters_18Sopenref96_GOMamazon.txt --prefilter_percent_id 0.0 -f
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One Response to Metagenomes (xeno, gom_fungi) and rerunning Open Ref OTUs

  1. So what happened? A little summary for those of us interested in Xenophyophore, who are not quite as versed in the details of DNA sequencing, would be nice.

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