# Workflow for illumina demultiplexed paired end data

**URL:** https://forum.qiime2.org/t/workflow-for-illumina-demultiplexed-paired-end-data/4832
**Category:** User Support
**Created:** [July 2, 2018, 2:10pm UTC](https://forum.qiime2.org/t/workflow-for-illumina-demultiplexed-paired-end-data/4832 "2018-07-02T14:10:02Z")
**Posts on this page:** 1
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### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [July 6, 2018, 2:10pm UTC](https://forum.qiime2.org/t/workflow-for-illumina-demultiplexed-paired-end-data/4832/3 "2018-07-06T14:10:59Z")

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Hi @Dharitri,  
Import the sequence files together into a single artifact of demultiplexed sequences, and go from there.

Import as described [here](https://docs.qiime2.org/2018.6/tutorials/importing/#fastq-manifest-formats) or [here](https://docs.qiime2.org/2018.6/tutorials/importing/#casava-1-8-paired-end-demultiplexed-fastq). Either will produce a single artifact of demultiplexed sequences that you can use downstream.

Then you can proceed with `qiime dada2 denoise-paired` or with OTU picking (if you use dada2 you can trim the primers out with the `trim` parameters. If you use OTU picking, first use `cutadapt trim-paired` as described [here](https://forum.qiime2.org/t/demultiplexing-and-trimming-adapters-from-reads-with-q2-cutadapt/2313) to trim primers before proceeding).

Good luck!

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