# Truncating reads with multiple sequencing runs and different primers
**URL:** https://forum.qiime2.org/t/truncating-reads-with-multiple-sequencing-runs-and-different-primers/4969
**Category:** User Support
**Tags:** dada2, trim, primers
**Created:** [July 10, 2018, 2:39pm UTC](https://forum.qiime2.org/t/truncating-reads-with-multiple-sequencing-runs-and-different-primers/4969 "2018-07-10T14:39:26Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@ninaxhua](https://forum.qiime2.org/u/ninaxhua)
#### Post date: [July 10, 2018, 2:39pm UTC](https://forum.qiime2.org/t/truncating-reads-with-multiple-sequencing-runs-and-different-primers/4969/1 "2018-07-10T14:39:26Z")
I read [here](https://docs.qiime2.org/2018.6/tutorials/moving-pictures/) that the read lengths must be the same for all sequencing runs being compared to avoid study-specific bias. If one sequencing run used V4 16S primers and a different run used V3+V4 16S primers, would that mean I must give both runs the same —p-trunc-len values when using DADA2 or Deblur? If so, what value would be an acceptable cut off point based on the quality plots that I included?
Also, originally I trimmed it based on the value 235 from the quality plot for the V4 only run, but if I use that value as a trimming cut off point for the V3+V4 run, would I be losing the part of the read that was amplified by the V4 primer?
After this step I was planning to merge both feature tables and sequences and use the fragment-insertion plug-in.
Thanks again!
**V4 only run**
**V4+V4 run**
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### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [July 10, 2018, 4:47pm UTC](https://forum.qiime2.org/t/truncating-reads-with-multiple-sequencing-runs-and-different-primers/4969/2 "2018-07-10T16:47:40Z")
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### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [July 10, 2018, 6:17pm UTC](https://forum.qiime2.org/t/truncating-reads-with-multiple-sequencing-runs-and-different-primers/4969/3 "2018-07-10T18:17:14Z")
> [@ninaxhua](#):
>
> read lengths must be the same for all sequencing runs being compared to avoid study-specific bias
depends what you want to do. See also the [q2-fragment-insertion tutorial](https://github.com/biocore/q2-fragment-insertion) (and read the paper at the bottom of the tutorial if that sounds like it fits your needs)
> [@ninaxhua](#):
>
> If one sequencing run used V4 16S primers and a different run used V3+V4 16S primers, would that mean I must give both runs the same —p-trunc-len values when using DADA2 or Deblur?
No, because the 5' primers are different. Instead, trim to the same primer sites. The best approach would be to use [`qiime cutadapt trim-paired`](https://forum.qiime2.org/t/demultiplexing-and-trimming-adapters-from-reads-with-q2-cutadapt/2313) to cut to the same sites prior to dada2 (this would require the primers to be present at the time of trimming).
> [@ninaxhua](#):
>
> Also, originally I trimmed it based on the value 235 from the quality plot for the V4 only run, but if I use that value as a trimming cut off point for the V3+V4 run, would I be losing the part of the read that was amplified by the V4 primer?
Since you have paired-end reads it does not matter where you truncate, so long as your reads are still merging successfully.
> [@ninaxhua](#):
>
> After this step I was planning to merge both feature tables and sequences and use the fragment-insertion plug-in.
Ah you have already found q2-fragment insertion. If so, you do not need to use the same dada2 parameters (specifically for q2-fragment-insertion... for other steps like taxonomy-based analyses you would need to do so).
Good luck!
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### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [July 10, 2018, 6:17pm UTC](https://forum.qiime2.org/t/truncating-reads-with-multiple-sequencing-runs-and-different-primers/4969/4 "2018-07-10T18:17:16Z")
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [August 11, 2018, 12:17am UTC](https://forum.qiime2.org/t/truncating-reads-with-multiple-sequencing-runs-and-different-primers/4969/5 "2018-08-11T00:17:20Z")
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