remove primers and update groups file

mothur bugs
1

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.

1 Like
2

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.

Pat