I am new to Miseq


I am new to Miseq and am struggling to work out how to set up my files and where to start on the usual QIIME workflow. We ran a 300bp paired end illumina run which was uploaded onto base space. I have downloaded the fastq files which are already demuliplexed and each sample has 2 reads.

Should i be concatenating these files? If so how and what would the set up be like? Or how do i input multiple files?
should i start from which stage to analysis?

best regards


Hi @elaheahmadi,

Have you see our importing tutorial? The fastq manifest format I linked to should be right for you.

Check out our other tutorials, particularly Atacama soils (a paired-end example) for examples. In your case, the reads are already demultiplexed, so start at denoising.

I hope that helps!

1 Like

Hey hey @elaheahmadi!

We have just the thing for you! Check out the new Overview tutorial that @Nicholas_Bokulich recently wrote up, this should give you a great high-level overview of what to do, and will point you at tutorials that will provide more specific detail regarding things like importing, etc. :qiime2: :t_rex:


This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.