Time of running DADA2

[Nicholas_Bokulich]

Thanks @ucassee. Could you please also provide me with the command that generates this error with these sequences? Please also send the QZA.

@ucassee

i still don’t understand why dada2 can’t be used to denoises joined reads.

Can DADA2 be carried on pre-joined reads

Hi @sindhu_mohandas, No actually, Dada2 will not perform properly if your reads are pre-joined with another tool. The main issue is that this is in conflict with the error-building approach utilized by Dada2. When you join reads you are assigning new quality scores (calculated differently between different tools) in the overlapping region which are not true q-scores which Dada2 uses. So, you want to run raw data without any prior modifications. What you've done is more appropriate for Deblur h…

https://github.com/benjjneb/dada2/issues/327#issuecomment-400038014