I have used Qiime2 to do analysis with paired-end, phred33 and multiplexed sequences, and everything went well after importing the raw data into qiime2 artifacts.
Now, however, I am trying to analysis the mock-6 data ( from the Mockrobiota GIthub ), includes barcodes.fastq.gz and forward reads in fastq format
which is a Phred64.
I was able to import this multiplexed data as “EMPSingleEndSequences” type,
qiime tools import \ --type EMPSingleEndSequences \ --input-path mock_6_data \ --output-path mock_6_data/mock.qza
and after I demultiplexed the data, the quality plot looks like this,
which obviously means I didn’t import the data correctly. So I am stucking in the very begining.