I am running ITSxpress for trimming ITS1 region for trimming data before classifying with UNITE database.
My workflow looks like this:
- Quality filtering of data;
- Removal of primer sequences (cutadapt)
- Import of paired-end data in QIIME2;
- 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,