Ramping up August analyses

Concatenated the re-demultiplexed GOM Illumina data from QIIME 1.7:

cat KO_1_1/seqs.fna KO_2_1/seqs.fna KO_3_1/seqs.fna KO_4_1/seqs.fna KO_5_1/seqs.fna KO_6_1/seqs.fna KO_7_1/seqs.fna KO_8_1/seqs.fna KO_9_1/seqs.fna KO_10_1/seqs.fna KO_11_1/seqs.fna KO_12_1/seqs.fna > GOM_concat1.7_fwd_demulti_1to12_1.fna
cat KO_1_2/seqs.fna KO_2_2/seqs.fna KO_3_2/seqs.fna KO_4_2/seqs.fna KO_5_2/seqs.fna KO_6_2/seqs.fna KO_7_2/seqs.fna KO_8_2/seqs.fna KO_9_2/seqs.fna KO_10_2/seqs.fna KO_11_2/seqs.fna KO_12_2/seqs.fna > GOM_concat1.7_rev_demulti_1to12_2.fna

Other things I did today:

  • Downloaded 18S Chimera data from Merlot
  • Downloaded HiSeq Metagenome data from Merlot
  • Downloaded Silva 111 and installed in Macqiime directory on both MacAir and iMac

Also running new open reference OTU picking on GOM Illumina fwd reads:

pick_open_reference_otus.py -i /Users/hollybik/Desktop/Data/Illumina_GOM/demultiplexed_qiime1.7/GOM_concat1.7_fwd_demulti_1to12_1.fna -o /Users/hollybik/Desktop/Data/Illumina_GOM/uclust_99_fwd -r /macqiime/silva_111/rep_set/Silva_111_full_unique.fasta --parallel -O 2 -s 0.1 --suppress_taxonomy_assignment --suppress_align_and_tree
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