Hi everyone, I have 300 paired-end fastq files for microbiome analysis. 20 of them have empty forward files, so I can only use their reverse counterpart. I want to know if I could import those 300 fastq as single end (280 as forward and 20 as reverse).
I tried this:
qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path RUN/manifest-single.csv --output-path RUN/UPSTREAM/single-end-demux.qza --input-format SingleEndFastqManifestPhred33
But I get this:
An unexpected error has occurred: Manifest for single-end reads can contain only forward or reverse reads, but not both. The following directions were observed: forward, reverse.
Is there any kind of importing method that allows what I want?
Thanks in advance