...
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”
| Code Block |
|---|
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.