# Combining data from different sequencing centers and primers

**URL:** https://forum.qiime2.org/t/combining-data-from-different-sequencing-centers-and-primers/4241
**Category:** User Support
**Tags:** dada2
**Created:** [May 22, 2018, 2:49pm UTC](https://forum.qiime2.org/t/combining-data-from-different-sequencing-centers-and-primers/4241 "2018-05-22T14:49:56Z")
**Posts on this page:** 1
**Showing post:** 15

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### Author: ![antgonza](https://forum.qiime2.org/user_avatar/forum.qiime2.org/antgonza/32/1236_2.png) [@antgonza](https://forum.qiime2.org/u/antgonza)
#### Post date: [May 25, 2018, 5:41pm UTC](https://forum.qiime2.org/t/combining-data-from-different-sequencing-centers-and-primers/4241/15 "2018-05-25T17:41:00Z")

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Hi @ninaxhua,

> [@ninaxhua](#):
>
> trimming both datasets to the same primer sites, dada2 separately, then merging?

To be honest, I haven't seen any published meta-analysis with DADA2 that combine different primers and sequencing technologies but that doesn't mean that they don't exist or it's not possible to generate them. Anyway, in my personal experience, we normally use close reference but in recent months we are moving to use deblur. In fact, the [fragment-insertion tutorial](https://github.com/biocore/q2-fragment-insertion#fragment-insertion-enables-meta-analyses-across-different-variable-16s-regions-and-fragment-length) is an example of deblur meta-analysis combining different regions.

> [@ninaxhua](#):
>
> So I would trim the run that used V3+V4 primers to the region that only includes V4? Would I trim off the adapter sequence and preceding bases?

Well, in theory this should work but in praxis I haven't seen great success using close-reference. I _believe_ this is due to the primer biases. However, I don't know if anyone has actually done this test with either DADA2 or deblur, perhaps worth checking, if this is something you are interested in.

> [@ninaxhua](#):
>
> The sequencing center that used the V4 primer linked [this](https://wikis.utexas.edu/display/GSAF/rRNA+bacterial+gene+and+fungal+ITS+metagenomics+samples) as their adapter sequences. Will the adapter sequence be the rRNA gene-specific primer sequences or Illumina platform-specific sequences?

I'm not sure I follow this question. Anyway, the primer normally is in the forward and sometime in the reverse read; however, this depends on the sequencing protocol (not the sample preparation where you add the primers). My suggestion will be to ask your sequencing center to be sure. BTW a lot of times is pretty easy to see if your primer is in your sequences cause you will see them "clearly" once you inspect your sequences.

> [@ninaxhua](#):
>
> I’m a little confused on where the fragment insertion plug in can be used?

Basically, fragment insertion is used after you get your denoised sequences (produced by DADA2 or deblur) and this seems to reduce the effect of the different primers at least based on the tutorial linked in my first answer in this message.

Hope this helps.

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