Make.contigs when primers weren't removed

Hi All, I’m reworking an older dataset that we had figured out but it isn’t working now. The short story is that we have demultiplexed files, but they still contain the primer sequences. In the past we ran make.contigs and then trim.seqs, but now when we run that series of commands it actually removes the site data from the count_table. In the original batch file we had, we were still using a mothur version that generated a groups file and I suspect that we were able to maintain the site information via the groups file, but now we aren’t so lucky. Any suggestions?

Hey Mario - Can you try using an oligos file with make.contigs? That should allow you to remove the primers. Alternatively, you could also design a reference alignment that does not include the primers and let align.seqs remove the primers for you.


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