Hello. I am new to using Qiime2 but attended a Qiime2 workshop in June. I successfully downloaded my demultiplexed sequences into Qiime2 from the sequencing facility website using the following command where "699" was the name of my flowcell: wget -nH --cut-dirs=1 -r -np -A 'fq.gz,fastq.gz,txt' --a…

Note to anyone following along, @Lisa_Crummett and I coordinated via DM today and sorted out the import issues by updating the manifest file (mainly excel was adding extra columns to the CSV), and tweaking the import command to reflect paired-end sequences: qiime tools import --type ‘SampleData[…

Hi @Lisa_Crummett ! [image] Lisa_Crummett: (1) the command to download my data (provided by the sequencing facility) is different than that specified in the tutorial No worries about this --- everyone's data is different, and as such, is fetched in its own special way. All that matters is tha…

Having just gone through this steps recently myself I thought I'd share quick tip. You can quickly find the absolute paths to your files that you need in the manifest file with: find 'pwd' /path/to/your/folder/containing/fastqs .htaccess That lists the absolute paths of all samples that you can ea…

Hi @Mehrbod_Estaki , thanks for posting that tip! Regarding a fastq variant detection script --- there are many one-liner scripts floating around on forums like biostars and seqanswers --- I would suggest looking there. If you have some ideas about implementing variant detection in QIIME 2, please s…

Great! Good to know that there's maybe a way of doing this. I have no suggestions as how this can be done myself as its outside my capabilities but maybe I'll post it as a suggestion as you recommended and hope it will generate some momentum for others to take on the task. I know lots of novice user…

Hello Mathew. I wish that I could chat with you or another Qiime2 tech over the phone... I have spent hours just trying to import my paired end data by using the command in the "Importing generic Fastq data" tutorial and I think the problem lies with Qiime2 not "seeing" my fasta files, which are sto…

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Denoising and trimming already demultiplexed paired end data

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