I am using Qiime2 v2019.1 in a high performance computing environment.
I am testing my 16S v3/v4 data using DADA2 on 2x300 paired end reads.
I tried running DADA2 denoise-paired trimming at 150bp in one iteration and again with no trimming in another iteration. With both trimming choices I ended up losing the majority of my reads during dada2 denoise-paired.
Here is a portion from my stats file for the 150bp trimming run:
sample-id input filtered denoised merged non-chimeric
#q2:types numeric numeric numeric numeric numeric
BMI-Plate10WellC10-16S 16502 252 252 0 0
BMI-Plate15WellE4-16S 13882 7841 7841 0 0
BMI-Plate20WellG10-16S 32631 25711 25711 91 90
BMI-Plate20WellH10-16S 23718 18336 18336 35 35
BMI-Plate20WellH7-16S 26738 20715 20715 76 76
BMI-Plate20WellH8-16S 35523 28328 28328 104 98
Here is a portion from my stats file for the 300bp run:
sample-id input filtered denoised merged non-chimeric
#q2:types numeric numeric numeric numeric numeric
BMI-Plate10WellC10-16S 16502 0 0 0 0
BMI-Plate15WellE4-16S 13882 0 0 0 0
BMI-Plate20WellG10-16S 32631 2 2 2 2
BMI-Plate20WellH10-16S 23718 3 3 0 0
BMI-Plate20WellH7-16S 26738 1 1 0 0
BMI-Plate20WellH8-16S 35523 1 1 1 1
I ran Cutadapt outside of Qiime to trim off the primers.
Here is what my plots look like for the imported data (primers already removed using Cutadapt).
After no success using DADA2 denoise-paired I decided to merge my reads myself outside of Qiime using FLASH after removing primers using Cutadapt and then used dada2 denoise-single which resulted in much better read retention. Here is a portion from my stats file running dada2 denoise single:
sample-id input filtered denoised non-chimeric
#q2:types numeric numeric numeric numeric
BMI-Plate10WellC10-16S 16502 8076 8076 8045
BMI-Plate15WellE4-16S 13882 6103 6103 6103
BMI-Plate20WellG10-16S 32631 16367 16367 16200
BMI-Plate20WellH10-16S 23718 12202 12202 12142
BMI-Plate20WellH7-16S 26738 14643 14643 14611
BMI-Plate20WellH8-16S 35523 20401 20401 20310
And my plot from merging the reads outside of DADA2:
My question is, what is happening when I try to run dada2 denoise-paired that is causing me to lose the majority of my reads?