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