GOM Picking OTUs…again

OK, finally re-demultiplexed the GOM OTUs, and concatenated everything together again. Before I did this I checked that each file was demultiplexed correctly, e.g. the sample FASTA header corresponded to what it was supposed to be per the sequencing facility report.

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_concat_fwd_demultirepeat_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_concat_rev_demultirepeat_1to12_2.fna

And then off to OTU picking. Starting with the reverse PE data this time, since the file is much smaller and I’ll hopefully have something to work with sooner.

pick_otus.py -i ~/GOM_demultiplexed/GOM_concat_rev_demultirepeat_1to12_2.fna -m uclust_ref -o /home/ubuntu/GOM_demulti2_rev_OpenRef_uclust99_12Oct -r /home/ubuntu/Silva_108/rep_set/Silva_108_rep_set_Eukarya_only.fna -s 0.99 –enable_rev_strand_match

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