# Removing sequence primers
**URL:** https://forum.mothur.org/t/removing-sequence-primers/2313
**Category:** Commands in mothur
**Created:** [March 23, 2015, 4:48am UTC](https://forum.mothur.org/t/removing-sequence-primers/2313 "2015-03-23T04:48:45Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@Alan\_Wong](https://forum.mothur.org/u/Alan_Wong)
#### Post date: [March 23, 2015, 4:48am UTC](https://forum.mothur.org/t/removing-sequence-primers/2313/1 "2015-03-23T04:48:45Z")
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
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### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [March 23, 2015, 3:58pm UTC](https://forum.mothur.org/t/removing-sequence-primers/2313/2 "2015-03-23T15:58:07Z")
The make.contigs command can remove the primers and assemble the reads for you, [http://www.mothur.org/wiki/Make.contigs](http://www.mothur.org/wiki/Make.contigs). Here’s a link to the oligos file format, [http://www.mothur.org/wiki/Oligos\_File](http://www.mothur.org/wiki/Oligos_File).