ITS data processing

[Nicholas_Bokulich]

@vpandyar

• Is there a difference to using ITSxpress vs cutadapt? Should I use one over the other or both sequentially?

Yes, big difference. Check out the ITSx or ITSxpress papers for more details; basically ITSxpress will trim to the ITS region itself whereas cutadapt is just trimming away adapters.

Use one or the other on your data, no need to do both.

@vpandyar

When using cutadapt do I use the adapter and primer sequence of both my forward and reverse primers?

You can. Depends if you want to trim away one or both.

@vpandyar

The cutadapt ITS tutorial mentions using the reverse complement - do I need to do that also and if so how if I have 2 different adapters/primers.

The tutorial already gives you that answer:

@Nicholas_Bokulich

Note that we trim the forward primer (just in case it is still on the front of our sequences) and the reverse complement of the reverse primer from the forward reads. We trim the reverse primer and reverse complement of the forward primer from the reverse reads.