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We generated otu tables for 16S and ITS, which can be found in the /project/microbiome/data/seq/psomagen_17sep20_novaseq2/otu/16S and /project/microbiome/data/seq/psomagen_17sep20_novaseq2/otu/ITS directories for all projects. The script to do this is /project/microbiome/data/seq/psomagen_17sep20_novaseq2/otu/run_slurm_mkotu.pl. This script crawls all of the projects (and loci) in the tfmerged/ folder, and concatenates all input sequences files and passes them through a UNIX pipe for analysis (rather than making another copy of all the sequence data). This was rerun on with the addition of line 5 (--search_exact) and --relabel 'otu' added to line 2. The key part the script is the job that is created for each project:
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$job .= "cat $tfmdirectory/*tfmergedreads.fa $tfmdirectory/joined/*tfmergedreads.fa | vsearch --derep_fulllength - --threads 32 --output uniqueSequences.fa --sizeout;\n";
$job .= "vsearch --cluster_unoise uniqueSequences.fa --relabel 'otu' --sizein --sizeout --consout zotus.fa --minsize 8 ;\n";
$job .= "vsearch --uchime3_denovo zotus.fa --nonchimeras zotus_nonchimeric.fa --threads 32;\n";
$job .= "cat $tfmdirectory/*tfmergedreads.fa $tfmdirectory/joined/*tfmergedreads.fa | vsearch --usearch_global - --db zotus_nonchimeric.fa --otutabout - --id 0.99 --threads 32 | sed 's/^#OTU ID/OTUID/' > 'otutable';\n";
$job .= 'vsearch --search_exact ${WORKDIR}/tfmergedreads.fa --db zotus_nonchimeric.fa --otutabout - --id 0.99 --threads 32'. " | sed 's/^#OTU ID/OTUID/' > 'otutable.esv';\n"; |
Make coligo table
In /project/microbiome/data/seq/psomagen_17sep20_novaseq2/coligoISD, there are 16S and ITS directories for all projects. These contain a file named coligoISDtable.txt with counts of the coligos and the ISD found in the trimmed forward reads, per sample. The file run_slurm_mkcoligoISDtable.pl has the code that passes over all of the projects and uses vsearch for making the table.
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