I am interested in analyzing paired end reads

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

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) to familiarise with the formats and commands.

Best wishes,
Luca