I have a problem with DADA2 (version 2019.4.0) in QIIME2 (qiime2-v2019.04) in conda: the merge results are poor. The region is V3+V4, the primers are 341F-806R. The primers are attached to the sequences. I took 3 samples for a tests. The original demux.qzv file is attached.
I used the following script in QIIME2:
qiime dada2 denoise-paired
The denoising-stats results:
F+R input filtered denoised merged non-chimeric
#q2:types numeric numeric numeric numeric numeric %
Shlomit001-Sh-Cn-0T-S1 40,340 33,272 26,315 14,905 13,547 34
Shlomit002-Sh-Cn-0T-S2 51,994 42,342 34,953 21,235 19,402 37
Shlomit003-Sh-Cn-0T-S3 45,586 37,210 31,013 18,938 17,263 38
Sequence length 400-425 bp.
Working with longer sequences --p-trunc-len-f 300 --p-trunc-len-r 289 , gave worse results.
I tried to use DADA2 in R for further possibilities, but it did not help.
I did DADA2 for forward files only, --p-trunc-len 286, and it doubled the recovery, but the sequences were shorter: 266 bp.
Are these results acceptable?
Is the sequencing is OK?
What can I do to improve the results?
demux.qzv (293.2 KB)