Too many reads lost in ITSxpress trimming

Library Plugin Support ITSxpress
1

Hi everyone,
I am running ITSxpress for trimming ITS1 region for trimming data before classifying with UNITE database.
My workflow looks like this:

  1. Quality filtering of data;
  2. Removal of primer sequences (cutadapt)
  3. Import of paired-end data in QIIME2;
  4. Trimming using ITSxpress

In the trimming step I am loosing too much of data (close to 90%), I also ran the data given in tutorial here , where the loss was ~12 %.
Can someone help me in understanding the reason behind this loss. And probably a way to retain more reads for dada2 denoising.

Thanks and regards,
Sudhir

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