I don't even know if the data I downloaded has been demultiplexed or not. I am a beginner. Please help me see if this data can be used for qiime2?
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@Thu_Th_y_Le,
I believe the convention for files uploaded to the SRA Archive is to have them already de-multiplexed, at least since 2017. However, if multiple runs were performed, then they often will be combined into the same file, this makes denoising with q2-dada2 problematic as it calculates error on a per sequencing run basis. You might want to checkout q2-fondue(github). It is designed for working with public data!
@misialq, one of its developers, would possibly be able to help you with questions that you might have regarding it. @SoilRotifer has worked with SRA data a lot more than I have and might be able to provide a bit better insight/a firmer answer about conventions and practices than I can.
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thank you so much, it's helpful to me
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