# Help Importing demultiplex paired end files with barcodes in head (only two files, files not separated by sample)

**URL:** https://forum.qiime2.org/t/help-importing-demultiplex-paired-end-files-with-barcodes-in-head-only-two-files-files-not-separated-by-sample/5639
**Category:** User Support
**Tags:** import
**Created:** [August 16, 2018, 10:10pm UTC](https://forum.qiime2.org/t/help-importing-demultiplex-paired-end-files-with-barcodes-in-head-only-two-files-files-not-separated-by-sample/5639 "2018-08-16T22:10:34Z")
**Posts on this page:** 1
**Showing post:** 2

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### Author: ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [August 17, 2018, 1:10pm UTC](https://forum.qiime2.org/t/help-importing-demultiplex-paired-end-files-with-barcodes-in-head-only-two-files-files-not-separated-by-sample/5639/2 "2018-08-17T13:10:02Z")

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Hey there @Jane_Lucas!

> [@Jane\_Lucas](#):
>
> There are only two files that contain the Forward and Reverse reads of all of my samples

Okay!

> [@Jane\_Lucas](#):
>
> I believe that the sequences have already been demultiplexed.

Maybe not - if there are only two files with all the samples in them, that indicates that things are still _multiplexed_.

> [@Jane\_Lucas](#):
>
> Also these sequences have the barcode included in the header, and I do not have a separate barcodes.fastq file.

Not having a separate barcodes file is fine, we have plenty of options to get around that, but they require that the barcodes are still present _in the read_ itself, rather than in the header. Is it possible the barcode is in both the header _and_ the read? If so, then check out this [community tutorial](https://forum.qiime2.org/t/demultiplexing-and-trimming-adapters-from-reads-with-q2-cutadapt/2313) for demultiplexing using q2-cutadapt.

If the barcodes are _only_ in the header, then you will need to find a way to demultiplex these reads prior to importing into QIIME 2, as we have no way to demux reads based on headers. Once demuxed, you could [import using the fastq manifest](https://docs.qiime2.org/2018.6/tutorials/importing/#fastq-manifest-formats).

Keep us posted! :qiime2: 🦖

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