I’m having a hard time trying to figure out how to import my data (single end, multiplex fastq file) to qiime2 since I only have the fastq and the mapping file with the #SampleID, BarcodeSequence, LinkerPrimerSequence and some other extra information.
Any help or tip will be very much appreciated.
Thank you all in advance,
Hey there @Fernanda_Costa!
Where are your barcodes, with respect to the fastq file? Are they in the reads? If so, you can use q2-cutadapt to demux, then proceed with denoising, etc. If they are in the header, then you will need to use some other tool for demuxing outside of QIIME 2, then import using a manifest format. If they aren't in the fastq file at all, then you might be hard-pressed to do anything with these data, since there is no way to associate reads with samples.
Take a peek at the overview tutorial at some point too, just to get your feet wet.
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