merging files from the shhh pipeline

Commands in mothur
1

I have 32 samples, but because the samples were sequences on two titanium plates, which both were divided in two i have only used 8 barcodes. Therefore i’m running the shhh.flows and trim.seqs commands four times. Is there an easy way to merge the resulting files (fasta, names, and group files) so i can do the rest of the pipeline as one dataset.
Anders

2

use the merge.groups command.

i.e.

mothur > merge.files(input=fileA.fasta-FileB.fasta-FileC.fasta, output=SAMPLE.fasta)

Hope this helps,
Chris