Hi everyone, I am using QIIME2 for some Fungal data with ITS1F and ITS2R primers. How do i know which region to cut with ITSXPRESS?
The choice is ITS1 or ITS2. I read papers where authors trim one or the other with no explanation why.
Hi @Mantella86 ,
This will depend on which primer set you used, and whether these primers amplify the ITS1 or ITS2 domains. Do a google image search for this, there are lots of nice primer maps out there on the internet.
Usually this is just implicit, as the position in the ITS region is known. They consulted a primer map to determine.
I recommend that you find a primer map to answer this question, as it will make your life easier in so many ways. But I will give you a hint: the primer names are usually arbitrary and to not necessarily correspond to the ITS domains that have the same names.
If you still cannot find an answer after consulting a map, feel free to reply with an image of the primer map that you found, and I could help orient you.
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