Trim MiSeq 16S sequencing primers from raw sequence?

[Rodney Sun]

Dear Everyone,

This may be a simple question about initial metagenomics data analysis with MiSeq 16S v34 sequencing primers.
Should we need to trim (forward and reverse) primer sequences locating in the start and the end of raw sequences? and Why?

In my opinion, primer sequence is a part of 16S rRNA sequence since the primer is used to target the specific conserved regions of 16S rRNA gene in order to catch the variable regions. Maybe it is not necessary to trim primer sequences from raw sequences for downstream analysis?!
However, the process ‘trim primer’ usually exists in some 16S sequencing data analyses (RDPipeline, mothur, etc.). Maybe the trimming process of these tools is specific for 454 pyrosequnecing?!

Hence, my doubt is which one is the most suitable for the first step in analyzing illumina 16S v34 paired-end reads:
1. Trim primers first and assemble illumina paired-end reads for downstream analysis.
2. Directly assemble illumina paired-end reads from raw sequence (fastq) for downstream analysis.

I do not find the specific question and the corresponding answer. I will be very glad if anyone provides any suggestions, helps or the posts which is discussed before.

Thank you!
Rodney

[cliffbeall]

The consensus in the field is that the best practice is to trim the primers, and this is built-in to software pipelines such as mothur.

PCR works relatively efficiently with a mismatch or two, so the primer derived sequence is not guaranteed to reflect the starting material.

[Rodney Sun]

The consensus in the field is that the best practice is to trim the primers, and this is built-in to software pipelines such as mothur.

PCR works relatively efficiently with a mismatch or two, so the primer derived sequence is not guaranteed to reflect the starting material.

cliffbeall, Thanks for your information. I think this is a rational explanation.