Organizing GOM Illumina data

Organizing GOM analyses run to data – downloaded completed runs onto 1TB external hard drive, along with parameter files (and copied command ran into a comment line at the top of the parameter file). Proceeding with more AWS analysis.

Forward reads at 96% (m2.4xlarge was running out of memory, so dropped down to 6 parallel jobs):

pick_open_reference_otus.py -i /home/ubuntu/data/GOM_concat1.7_fwd_demulti_1to12_1.fna -o /home/ubuntu/data/uclust_openref96_fwd_16Sept -r /home/ubuntu/data/silva_111/99_Silva_111_rep_set_euk.fasta --parallel -O 6 -s 0.1 -p /home/ubuntu/data/qiime_parameters_18Sopenref96_GOMamazon_16sept.txt --prefilter_percent_id 0.0

(9/20/13) Forward reads at 99% – kept at 6 parallel jobs

pick_open_reference_otus.py -i /home/ubuntu/data/GOM_concat1.7_fwd_demulti_1to12_1.fna -o /home/ubuntu/data/uclust_openref99_fwd_20Sept -r /home/ubuntu/data/silva_111/99_Silva_111_rep_set_euk.fasta --parallel -O 6 -s 0.1 -p /home/ubuntu/data/qiime_parameters_18Sopenref99_GOMamazon_16sept.txt --prefilter_percent_id 0.0

Reverse reads at 99%:

pick_open_reference_otus.py -i /home/ubuntu/data/GOM_concat1.7_rev_demulti_1to12_2.fna -o /home/ubuntu/data/uclust_openref99_rev_16Sept -r /home/ubuntu/data/silva_111/99_Silva_111_rep_set_euk.fasta --parallel -O 8 -s 0.1 -p /home/ubuntu/data/qiime_parameters_18Sopenref99_GOMamazon_16sept.txt --prefilter_percent_id 0.0
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2 Responses to Organizing GOM Illumina data

  1. Jaz says:

    HI Holly, did you have paired-end data? If so, how did you set up your 2 read in a merged file? also did you create a mapping file? sorry i am learning and you may be able to help.

    • hollybik says:

      We have custom scripts in the lab to merge reads (since old versions of QIIME didn’t support paired-end data). However, the newest version of QIIME 1.8 does now support paired end data, so you can now input both files and merge/QC them within QIIME itself.

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