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
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).