Using ITSXPRESS advice

[Mantella86 (Martyn)]

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.

Regards

Martyn

[Nicholas_Bokulich]

Hi @Mantella86 ,

@Mantella86

How do i know which region to cut with ITSXPRESS?

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.

@Mantella86

I read papers where authors trim one or the other with no explanation why.

Usually this is just implicit, as the position in the ITS region is known. They consulted a primer map to determine.

@Mantella86

I am using QIIME2 for some Fungal data with ITS1F and ITS2R primers

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.

Good luck!