Separate groups

Commands in mothur
1

Hi everyone,
I have my output files (fasta, qual, report and groups) from the make.contigs commands, but my original input Fastq file contains raw sequences from two different experiments that even use two different primers sets, my question is, if is possible in this point to create two new separated fasta and group files of the two experiments for the further analyses?

Thank you for the help,
Sebastián

2

You would have to do it before running make.contigs. In your oligos file you can assign the primers names as well. It would look like:

primer CCTACGGGAGGCAGCAG ATTACCGCGGCTGCTGG V3
primer ATTAGAWACCCBDGTAGTCC CCCGTCAATTCMTTTRAGT V5
primer ACTYAAAKGAATTGACGGG ACRACACGAGCTGACGAC V6
…

Mothur would create group names like:

seq1 barcodeName.primerName