# DADA2 Merge problems **URL:** https://forum.qiime2.org/t/dada2-merge-problems/11904 **Category:** User Support **Created:** [October 10, 2019, 2:01pm UTC](https://forum.qiime2.org/t/dada2-merge-problems/11904 "2019-10-10T14:01:46Z") **Posts on this page:** 1 **Showing post:** 7
### Author: ![yanxianl](https://forum.qiime2.org/user_avatar/forum.qiime2.org/yanxianl/32/2039_2.png) [@yanxianl](https://forum.qiime2.org/u/yanxianl) #### Post date: [November 7, 2019, 10:15am UTC](https://forum.qiime2.org/t/dada2-merge-problems/11904/7 "2019-11-07T10:15:22Z")
> [@Shlomit](#): > > I tried a range of trunc-len values in F and R. The best results were f260 r220, after trimming the primers. > > Is it like ca f280 r240 if I would do the analysis without trimming the primers with cutadapt? Hi, assuming that cutadapt trimmed off the first 20 bases of your froward and reverse reads, then you're right. Note that [primer sequences in the reads can interfere with both merging and chimera removal](https://forum.qiime2.org/t/loss-of-data-with-dada2/3006/5). Make sure that you correctly removed the primer sequences. > [@Shlomit](#): > > The best results were 32-37% recovery. Not very good. Losing a large fraction of your reads may not necessarily be a bad thing. Check [this comment by Dr. Benjamin Callahan](https://forum.qiime2.org/t/lost-of-data-with-dada2/1449/9). You can run a rarefaction analysis to find out if the resulting sequences are enough for the downstream analysis for most of your samples. If that's the case, then you're fine. > [@Shlomit](#): > > I got similar merge results in another project, from another working group. It looks like DADA2 problem. The lost of large fraction of reads is more likely caused by the data than the DADA2 pipeline. To verify that, you can download some similar data with mock, denoise the sequence with the QIIME2 version you're using and see what you get. If the mock looks as it should be, then it's not the DADA2's problem. > [@Shlomit](#): > > Do you suggest to accept the results, (32-37% recovery), or do the analysis on Foreword sequences only, or do something else? As mentioned above, a positive control helps you to find out if there's something wrong with the bioinformatics. You can test your ideas with the mock sample if you happened to include one in your sequencing run. If not, you may want to go ahead with both approaches and judge the results with your knowledge about your samples. Use the one that makes sense to you. -Yanxian --- _[View the full topic](https://forum.qiime2.org/t/dada2-merge-problems/11904)._