I have a couple questions. I know that they are probably very simple but I am still new to this and could use all the help I could get. I have demultiplexed fastq data for every sample of a study (amplicon 16sRNA Data) and I am stuck in how I can import the data into Qiime2 from a folder on my machine? Also btw I am using Qiime2 on a VM in virtual box. Then from there, if you have the time, could you also tell me how I can take the fastq data and make an OTU table from it? Is there a way to know which amplicon data directory is best?
Wecome to the forum! One of my favorite places to start on QIIME is with the tutorials.
You will need to get the data into your virtual box; (I will fully admit Ive never done this, but google suggests a couple solutions including this one… but please check back if you cant figure it out.)
Then, I would build yourself a manifest file. Casava will look easier; ignore the trap and just go with the manifest first. There’s even a nifty little automated manifest generator for R.
After you import your data, you can look at a summary to see what the quality looks like.
And here we get back to the tutorials! The moving pictures and PD mice will walk you through a common 16s rRNA analysis with maybe a little bit of interpretation thrown in along the way. If you want ASVs (more precision that OTUs and IMO more appropriate given that its almost 2020 and OTUs are so 2015), you can either chose DADA2 if you have unfiltered, unjoined data (The Atacama Soils tutorial goes through this with DADA2, the Alternative Methods of read joining shows Deblur). Or, if you do decide to go with OTUs, there’s a whole tutorial about that!
I have made a python3 manifest maker too which I know still works!
Not 100% sure about the R one as I haven’t been checking and updating it with new qiime versions.