Removing sequence primers

Commands in mothur
1

Hi all,

I recently got some Bacteria sequence using MiSeq and 27F/519R primers.

I was told that I need to remove the primers from the fastq files.

I would like to ask how do I do that?

Below is my pipeline

Step 1
fastq.info(wholesample.txt) <-- This will make all my samples into forward and reverse fasta files (10 samples)

Output: fasta files, each samples with forward and reverse fasta (sample 1 forward.fasta, sample 1 reverse.fasta, sample 2 forward.fasta, sample 2 reverse.fasta…)

Step 2:
trim.seqs(fasta=sample 1 forward.fasta, oligos=forward primer.oligos)

Do I need to trim away the primers the files one by one?

And afterwards do I need to make it back to fastq by make.fastq command?

Then proceed with make.contigs with the samples with primers trimmed away?

Also, I am not sure for the oligos files, do I need to make a paired primer oligos, or do I make a oligos file like below?:

forward ACCGTTAC…
reverse ACTTCCCC…

I am not sure how to trim away the primers for analysis. Thank you in advance

2

The make.contigs command can remove the primers and assemble the reads for you, http://www.mothur.org/wiki/Make.contigs. Here’s a link to the oligos file format, http://www.mothur.org/wiki/Oligos_File.