Thanks for your help! Yes, I found a solution. After I demultiplex my Paired-end data, I used the the “Atacama soil microbiome” tutorial to run Dada2 workflow. I check the tutorials and read the help file of Dada2, I think dada2 will run the QC, clean the chimaeras, join the paired end reads and build a feature table (which is roughly equivalent to OTU table in QIIME1). I just have some questions about the dada2 workflow results.
1> I got a feature table like your tutorial (https://view.qiime2.org/visualization/?type=html&src=https%3A%2F%2Fdocs.qiime2.org%2F2019.10%2Fdata%2Ftutorials%2Fatacama-soils%2Ftable.qzv).
If you check the link, you will find that there are 2 items – Number of features are 414 and Total frequency is 16,443.
I’m not sure how to interpret the results? Is feature meaning the observed OTU in QIIME1, right?
What about frequency? The total number of reads pass the QC, removed chimera, and after joined. The final reads counts of all samples?
2>Is it possible that I can get the the information by each sample. For example, sample before QC 10000reads, after QC 8000 reads, after joined 7000, after Chimera checking 6000 reads.
Basally, I want to know if the number of reads pass dada2 process by each sample. I want to know how many reads that I lost.
I check denoising-stats.qza file like this (https://view.qiime2.org/visualization/?type=html&src=https%3A%2F%2Fdocs.qiime2.org%2F2019.10%2Fdata%2Ftutorials%2Fatacama-soils%2Fdenoising-stats.qzv). However, some results don’t make a lot of sense to me.
For example, BAQ2420.2, after denoising ,you got 476 reads, but after join, you have got 244? How could it be? If you have 476 reads, the maximum number of joined pair would 476/2=238, right?
3> does the columns order reflect the actual dada2 workflow order?
The workflow order is fitering–>denoising–>merge(join)–>chimeric check
4>The last question about dada2 chimeric check. I used Vsearch to do a lot of chimeric checking (denovo checking) before, I didn’t use vsearch to do OTU clustering.
There is no much information about dada2 chimeric check parameters? It does it automatically? Is it denovo or using database?
I know QIIME2 supports vsearch plugin too, but it normally uses vsearch to do traditional OTU picking methods. Would it be possbile I can only run vsearch again to check the chimaeras? If I can? which artifacts I should use before dada2 workflow or after the workflow.
Generally, I trust vsearch for chimeric checking. I want to use most of steps of dada2 workflow, except for the chimeric checking. Can I do this?