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?
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!
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.
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