Content Comparison

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cd /project/microbiome/data/seq/gtl_tests/TRNL_Test/tfmergedreads/16S/TRNL1/trimmed

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sed -n '1~4s/^@/>/p;2~4p' ./*.fq > ./TrnlTest16S.favsearch -derep_fulllength --input TrnlTest16S.fa --output uniqueSequences.fa --sizeout --sizein

vsearch --derep_fulllength $s TrnlTest16S.fa \
        --strand plus \
        --output $s derep.fa \
        --sizeout \
        --uc $s.derep.uc \
        --relabel $s. \
        --fasta_width 0

vsearch --cluster_unoise derep.fa --centroids zotus_vsearch.fa --sizein --sizeout

Bioinformatics v2:

Reran 1st attempt commands starting with “./run_slurm_mergereads.pl“

Edited “215” in the below code chunk of trim_merge.pl to “115”

system("vsearch --fastx_filter $R1tmpA --fastq_trunclen 215 --fastqout $R1tmpB --threads 32");
system("vsearch --fastx_filter $R2tmpA --fastq_trunclen 215 --fastqout $R2tmpB --threads 32");
print "vsearch step1 complete\n";
if(-e $R1tmpB && -e $R1tmpB){ 
    system("vsearch --fastq_join $R1tmpB --reverse $R2tmpB --fastaout $joinedfile --threads 32");
    unlink($R1tmpA, $R2tmpA, $R1tmpB, $R2tmpB);
}

This fixed the merged and joined data for 16S, but not TRNL.