# Clarify on demux emp-paired
**URL:** https://forum.qiime2.org/t/clarify-on-demux-emp-paired/5565
**Category:** User Support
**Created:** [August 13, 2018, 9:57pm UTC](https://forum.qiime2.org/t/clarify-on-demux-emp-paired/5565 "2018-08-13T21:57:22Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@WAS1](https://forum.qiime2.org/u/WAS1)
#### Post date: [August 13, 2018, 9:57pm UTC](https://forum.qiime2.org/t/clarify-on-demux-emp-paired/5565/1 "2018-08-13T21:57:22Z")
Continuing the discussion from [Demultiplexing paired end read, trimming adapters and barcodes](https://forum.qiime2.org/t/demultiplexing-paired-end-read-trimming-adapters-and-barcodes/3639/3):
> [@Demultiplexing paired end read, trimming adapters and barcodes](https://forum.qiime2.org/t/demultiplexing-paired-end-read-trimming-adapters-and-barcodes/3639/3):
>
> You’ll want to use `qiime demux emp-paired` .
>
> Which primers were used doesn’t matter to this step, what’s more important is that your data has the non-biological data already stripped. In other words, the linker, primer, barcode, etc, are not in `R1` or `R2` (barcodes should be in `R3` ). It will use the order of `R3` to work out which sequences from `R1` and `R2` belongs to which samples.
>
> `qiime cutadapt demux-paired` is for when your barcodes are still in the sequences and need to both be identified and trimmed out. This shouldn’t be the case with an EMP-like protocol.
@ebolyen, would you say qiime cut-adapt demux-paired should still be applied after qiime demux emp-paired just to remove adapters
or
does demux emp-paired actually removes barcode while demultiplexing which are generally placed after the adapters?
Thank you for the good work
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### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [August 13, 2018, 9:57pm UTC](https://forum.qiime2.org/t/clarify-on-demux-emp-paired/5565/2 "2018-08-13T21:57:29Z")
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### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [August 14, 2018, 12:06am UTC](https://forum.qiime2.org/t/clarify-on-demux-emp-paired/5565/3 "2018-08-14T00:06:14Z")
Hey @WAS1!
> [@WAS1](#):
>
> @ebolyen, would you say qiime cut-adapt demux-paired should still be applied after qiime demux emp-paired just to remove adapters
No, you wouldn't demultiplex twice, you might use `cutadapt trim-paired` _if_ your sequencing protocol was not EMP (but sufficiently similar that emp-paired successfully demuxed your reads). I don't think I've seen that before.
Otherwise, using `cutadapt demux-paired` will remove the barcodes, but not necessarily the primer.
Setting a trim-left parameter in dada2 is usually sufficient since the primer is of a known length. In some cases you might need to get rid of your reverse-complemented reverse-primer on your forward reads (and vice-versa) if your amplicon is sufficiently variable that you tend to sequence over the reverse primer in the forward direction. That's where `cutadapt trim-paired` is handy.
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### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [August 14, 2018, 12:06am UTC](https://forum.qiime2.org/t/clarify-on-demux-emp-paired/5565/4 "2018-08-14T00:06:16Z")
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [September 14, 2018, 6:06am UTC](https://forum.qiime2.org/t/clarify-on-demux-emp-paired/5565/5 "2018-09-14T06:06:19Z")
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