Hello,
I am new to Bioinformatics and QIIME 2. I am trying to analyze some 16s sequencing data. I got my sequencing done by Novogene. I have received the fastq files from them (clean reads after filtering low-quality and chimeric reads). They used the FLASh software to merge the paired-end reads to single end reads. I am not sure what command I should use for importing these files into qiime. Is it
qiime tools import
--input-path manifest.tsv
--type 'SampleData[SingleEndSequencesWithQuality]'
--input-format SingleEndFastqManifestPhred33V2
--output-path se-demux.qza
or
qiime tools import
--input-path manifest.tsv
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-format PairedEndFastqManifestPhred64V2
--output-path paired-end-demux.qza
Thanks