ITS2 primers trimming without the primers sequences

The sequencing facility told me that their ITS2 primers are proprietary, so they cannot provide the sequences, but only the length of the primers. But, the sequences of the primers are needed to trim out the read-through to the opposite primers according to the ITS workflow (Fungal ITS analysis tutorial and

Is there any possibility to check if there are read-throughs and trim them out with only the length of the primers?

Thank you :sweat:

Hi @Lavendel,
See also the q2-itsxpress tutorial, this plugin can also handle readthrough and trimming to the ITS region, without knowing the actual primers:

That is very unfortunate. That is the antithesis of science, which should be reportable and reproducible by others. And causes so many problems like the one you are experiencing now! Fortunately, I think q2-itsxpress will save the day.

Let us know!


Thank you very much! :grin:

Yes, ITSxpress uses the edges of the ITS region (ITS1 or ITS2) so it does not need the primers.

If you need the primer sequences ( at least in the hybridizing regions) you can extract them using BBtools-BBmerge: in=reads.fq out=merged.fq adapters=adapters.fa