Demuliplex-sequences still contan primers, how can you run DADA2?

[Cheng50373640 (Cheng)]

Hi, everyone,

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!

regards
Jackie

[thermokarst]

Hi @Cheng50373640!

@Cheng50373640

How can you run DADA2 after import demuliplexed sequences?

The q2-dada2 methods actually only accept demultiplexed sequences as input, so this is perfect!

@Cheng50373640

because they still contain primers or/and barcodes.

You can use the q2-cutadapt plugin to remove primers or barcodes. Check out this community tutorial for examples.

Hope that helps!

[Cheng50373640 (Cheng)]

hi @thermokarst,

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!

[thermokarst]

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!