How to denoise 16s rRNA gene sequences with different primers?

Is it possible to integrate paired-end sequences with different primers? For example, if my sequences were sequenced in three runs (different primers and sequence length) and cover three different regions (V3, V4, V3-V4), how to generate infer sequence variants from these sequences using DADA2. Can I process as following : 1. trim, filter and denoise (dada) sequences from each run sepately 2. merge paired reads from each run seprately 3. merge separate runs 4. infer ASV.
I am confused about this problem. I'd appreciate some help.

Do I have to trim sequence in the same region after merging paired seqs and before infer ASV, i.e. trim V3-V4 region to V4, remain V4 region sequence, and abandon V3 region sequence.

Hello Kevin,

Is it possible to integrate paired-end sequences with different primers?

Yes, but there are some limitations to be aware of.

If you want to have shared ASVs across primers, then yes, you will need to trim to the exact same region across all three runs.

So you can choose to trim to the same region to get one unified ASV table, or you can process all three samples separately, and end up with three ASV tables.

You are not the first person to have this problem! Check out this thread where another teams is working with data from multiple variable regions.

Let me know if that helps answer your question!
Colin

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