How can you run DADA2 after import demuliplexed sequences? because they still contain primers or/and barcodes.
from the QIIME2 workflow, no plugin is used to cut primers or barcodes after importing demuliplexed sequences (deal with demu.qza file), so it’s real difficult to use qiime 2 if you have demuliplexed data from sequencing center.
does anyone have a good solutions which is easy to handle? thanks in adance!
The q2-dada2 methods actually only accept demultiplexed sequences as input, so this is perfect!
You can use the q2-cutadapt plugin to remove primers or barcodes. Check out this community tutorial for examples.
Hope that helps!
I’ve trimmed the primers, and tried many trimming strategies, but still only ~40% of total sequences out after DADA2 procedure,
I’m wondering it’s normal or not? thanks in advance!
I don’t think that is cause for concern, but there are so many factors that go into this!
- What does your
demux summarize plot look like before DADA2?
- What trim/trunc params did you run DADA2 with?
- What does your denoising-stats output look like (you would need to run in QIIME 2 2018.4 for that)?
If you want to share any of that, we can start to discuss specifics. Thanks!
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