Only half reads pass DADA2 denoise

[timanix (Timur Yergaliyev)]

Hi,

@Wei_Zhang

As this sequencing is completed on NovaSeq6000 which adopts binned quality scores, I wonder whether qimme2 DADA2 is still well compatible with those data?

NovaSeq6000 data still can be processed by Dada2 "as it is". More details here.

@Wei_Zhang

1. After DADA2 denoising, only half of the reads remained. I am not sure whether it is normal or not.

based on your stats output, around 85% of reads are passed through the filters (issue not in the binned quality scores), 75% are merged (truncating parameters are ok, though you still can try to improve it), and only 50% passed chimera detection filter. That means that a lot of your reads are considered to be chimeric. I would go back to the primers removal step to make sure that all of them are deleted.

Best,