Trouble importing data

I am very new to Qiime2. I have been reading and learning the step by step tutorials. However, I am lost just trying to figure out the sequencing data I received. I have about 96 samples, paired end which was demultiplexed by the sequencing company. When I received the data, the samples were seperated into each folder by the sample name and only one fastq.gz file. I am not sure what this file is. Is it alligned already? Which tutorial specifically can I follow for this kind of files?

Welcome to the forums! :qiime2:

That looks like demultiplexed fastq data to me. Take a look at the fastq manifest format, which would be perfect for that type of file. Try using --input-format PairedEndFastqManifestPhred33V2 that see if that works well.

Once imported, you can continue to use the following steps shown in the tutorials. Let us know what you try next and if you have any questions.

Thank you so much for the guidance! it took me a while (just 6 hours xD ) but i got the data imported. I could not use the "clean" data with only one fastq file though as i kept getting the error that it is not a Paired End file (I am not sure why this was so as the tutorial mentioned that reverse column was optional) so instead i went back to use the demultiplexed raw data which had both forward and reverse reads. I created the manifest file according to the tutorial and used

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /home/shaktee/BSF/manifest/manifest.tsv --output-path paired-end-demux.qza --input-format PairedEndFastqManifestPhred33V2

and it worked!! THANK YOU.

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I'm glad you got this working!

This is great:

This means that all the filtering and processing you do to the data will be recorded in the Qiime2 provavance files, which is great!

If you have more questions, feel free to ask them here or open another thread. :thread:

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