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:
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!!