Hello Qiime2 experts,
I have a set of fastq.gz files of 50 environmental samples; they are already demultiplexed, primer-clipped and merged by BBmerge. I thought I should be able to import them using this procedure, but there are two points where I’m not sure whether I have used the correct specification (marked with ### below)
qiime tools import
–type ‘SampleData[SequencesWithQuality]’ \ ### is this correct for fastq.gz files
–input-path Manifest.csv
–output-path import_results.qza
–source-format FastqGzFormat
Manifest.csv
sample-id,absolute-filepath,direction
sample-1,$PWD/some/filepath/sample1_merged.fastq.gz,forward ### should it be ‘forward’ or 'merged’
etc.
Thank you for your suggestions!
Alfons