ITS2 primers trimming without the primers sequences

[Nicholas_Bokulich]

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:

Q2-ITSxpress: A tutorial on a QIIME 2 plugin to trim ITS sequences

ITSxpress: a QIIME 2 plugin to trim ITS sequences Adam R. Rivers - USDA Agricultural Research Service Sveinn V. Einarsson - Dep. Microbiology and Cell Science, U. Florida & USDA Agricultural Research Service Background The internally transcribed spacer (ITS) region a widely used phylogenetic marker for fungi and other taxa. Previous work by Nilsson et al. (2009) showed that removing the conserved regions around the ITS results in more accurate taxonomic classification. An existing program, ITS…

@Lavendel

The sequencing facility told me that their ITS2 primers are proprietary

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!