NS5 Blank Alternate Approach

Owned by Gregg Randolph
Last updated: Sept 15, 2022
1 min read

Combine all easily located blanks

cd /project/microbiome/data/seq/cu_29april22novaseq5/tfmergedreads/16S/AIR21 cp *blank* *Blank* *BLANK* /project/microbiome/data_queue/seq/GtlAnalyses/NS5/tfmergedreads/ cd joined cp *blank* *Blank* *BLANK* /project/microbiome/data_queue/seq/GtlAnalyses/NS5/tfmergedreads/joined cd ../trimmed cp *blank* *Blank* *BLANK* /project/microbiome/data_queue/seq/GtlAnalyses/NS5/tfmergedreads/trimmed cd ../../MAWC21 cp *blank* *Blank* *BLANK* /project/microbiome/data_queue/seq/GtlAnalyses/NS5/tfmergedreads/ cd joined cp *blank* *Blank* *BLANK* /project/microbiome/data_queue/seq/GtlAnalyses/NS5/tfmergedreads/joined cd ../trimmed cp *blank* *Blank* *BLANK* /project/microbiome/data_queue/seq/GtlAnalyses/NS5/tfmergedreads/trimmed cd ../../SM19FIRE cp *blank* *Blank* *BLANK* /project/microbiome/data_queue/seq/GtlAnalyses/NS5/tfmergedreads/ cd joined cp *blank* *Blank* *BLANK* /project/microbiome/data_queue/seq/GtlAnalyses/NS5/tfmergedreads/joined cd ../trimmed cp *blank* *Blank* *BLANK* /project/microbiome/data_queue/seq/GtlAnalyses/NS5/tfmergedreads/trimmed

Rerun run_slurm_mkotu.pl on these

./run_slurm_mkotu.pl

Assign taxonomy

cd /project/microbiome/data_queue/seq/GtlAnalyses/NS5/otu/ salloc --account=microbiome -t 0-08:00 --mem=500G module load swset/2018.05  module load gcc/7.3.0 module load vsearch/2.15.1 vsearch --sintax zotus.fa --db /project/microbiome/users/grandol1/ref_db/gg_16s_13.5.fa -tabbedout Blanks_16S_NS5.sintax -sintax_cutoff 0.8

Output:  

Reading file /project/microbiome/users/grandol1/ref_db/gg_16s_13.5.fa 100%

1769520677 nt in 1262986 seqs, min 1111, max 2368, avg 1401

Counting k-mers 100%

Creating k-mer index 100%

Classifying sequences 100%

Convert into useful form:

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