Too many reads lost in ITSxpress

Hi everyone,
Sorry for raising the same issue again, but I could not get any responses in my previous post and it was closed in 30 days. Probably because it was posted during new year time.
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,

Good afternoon,

Thank you for your patience. Many people were off during the new year but we are back now!

That is high!

That is more expected.

In which of those 4 steps is 90% of the data being lost? Filtering, cutadapt, and ITSxpress could all remove data, so knowing which step is removing too much will help us know what to try next.


Hi @colinbrislawn,
Thanks for your response. I started with 81,022,719 (paired reads), the initial QC left me with 77,370,389 reads (95.49 % retained), after that, I trimmed the primer sequences and imported data to qiime2 (73,795,023 reads in total), then after trimming in ITSxpress I got 5622889 reads (~7.61 % remaining).
Will it make sense if I don't use ITSxpress and directly try assigning taxonomy on full length UNITE classifier?

Well, there's your issue! Something is wrong with ITSexpress :upside_down_face:

Yeah, try denoising with DADA2 without ITSxpress first.


This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.