# I am interested in analyzing paired end reads
**URL:** https://forum.qiime2.org/t/i-am-interested-in-analyzing-paired-end-reads/21396
**Category:** User Support
**Created:** [November 19, 2021, 2:23am UTC](https://forum.qiime2.org/t/i-am-interested-in-analyzing-paired-end-reads/21396 "2021-11-19T02:23:55Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@jgcx](https://forum.qiime2.org/u/jgcx)
#### Post date: [November 19, 2021, 2:23am UTC](https://forum.qiime2.org/t/i-am-interested-in-analyzing-paired-end-reads/21396/1 "2021-11-19T02:23:55Z")
If I am interested in analyzing paired end reads would a first command line such as the one below work? I have a text document with 4 forward primers and a document with reverse primers. Would I need a different input command for each forward primer and each reverse primer?
qiime tools import
--type MultiplexedPairedEndBarcodeInSequence
--input-path /location of the document/name of computer/file location of the document in the computer/name of the raw sequencung file.fastq.gz
--input-path /location of the document/document name containing the 4 forward primers.fastq.gz
--input-path /location of the document/document name containing the reverse primer.fastq.gz
--output-path multiplexed-seqs.qza
---
### Author:  [@llenzi](https://forum.qiime2.org/u/llenzi)
#### Post date: [November 19, 2021, 1:27pm UTC](https://forum.qiime2.org/t/i-am-interested-in-analyzing-paired-end-reads/21396/2 "2021-11-19T13:27:10Z")
Hi @jgcx,
Unfortunately that won't work! You will need more then one step,
first to import the sequencing data (which may change if your data are demultiplexed or not); then, if you have already demultiplexed data, you can trim the primers; else you need to demultiplex then you can trim primers.
The only possible caveat on the data demultiplexing step: you can perform it within QIIME2 only if you have same barcode in both forward and revers; if not (e.g. you have a combinatorial design), you need to demultiplex outside QIIME2 and import the sample files already demultiplexed (the easy way is by importing with a manifest file).
I suggest to start form the tutorials available ([Tutorials — QIIME 2 2021.8.0 documentation](https://docs.qiime2.org/2021.8/tutorials/)) to familiarise with the formats and commands.
Best wishes,
Luca
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [December 20, 2021, 7:27pm UTC](https://forum.qiime2.org/t/i-am-interested-in-analyzing-paired-end-reads/21396/3 "2021-12-20T19:27:32Z")
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.