remove primers and update groups file

My raw data consists of illumina reads in fastq files that are separated by sample but the primers have not been removed. Is there a route for analyzing these sequences in mothur?

I have tried make.contigs and trim.seqs, but:

  • since I do not have barcodes to remove, I cannot figure out how to get make.contigs to remove primer sequences.
  • I tried using trim.seqs to remove primer sequences, but that route did not update the groups file to reflect sequences removed because they did not have the primer sequences. This became a problem at the count.seqs step in the miseq sop workflow, which generated the following error:

[ERROR]: processes reported processing 22973793 sequences, but group file indicates you have 23525510 sequences. Either you have a file mismatch or a process failed to complete the task assigned to it.

You can remove primers in make.contigs with an oligos file. You can also use trim.seqs if you give it the oligos file and the group file from make.contigs.