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
--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
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.
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