How to deal with the demultiplexed and quality controlled data

Dear all,

I got a set of pair end data, which is demultiplexed, with low quality sequence removed, adaptor, barcode and primer trimmed, but haven’t been joined yet.

As I know (I am not sure actually), DADA2 has its own algorithm to remove the low quality sequence and to join the read1 and read2, generating representative sequence for the downstream analysis. So I think the best data for DADA2 may be the demultiplexed data with only barcode and primer trimmed. But what can I do with my data which has been quality controlled?

I do tried to import the the data and applied the DADA2, but got the unsatisfied results because almost 30% of the sequences were removed:

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May I know is there any other way I can obtain the representative sequence and the feature table from my data?

Thanks for all the ideas and suggestions!!

Hello @sage12

Thanks for telling me more about your data set.

While your reads have been filtered for quality, DADA2 has it’s own setting for quality filtering and error correction, so I would expect more of your reads to be removed. After all, I think it’s good that your data set is built with only the highest quality data. I would continue with analysis and see what you find in your data!

You could also try one of the other alternative plugins for processing your data, like deblur:

P.S. Happy New Year! :clinking_glasses:

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