RE: Would there be a reason to truncate the forward and reverse reads at different points?

[nbezia01 (BEZIAT Naëma)]

Would there be a reason to truncate the forward and reverse reads at different points?

Hi @msport469, You can absolutely truncate the forward and reverse in different places if there's a different drop off in quality. I do it often when my forward reads are high quality and the reverse reads have a lower drop in quality. In fact, this is a common behavior in Illumina data. There is one caveat: If you trim your reverse data too much, you may no longer be able to overlap enough to join the ends. So, just watch your trim length if you want to join reads. Best, Justine P.S. I mov…

Hello,
I have the same problem, I saw your advice, and I have a question
I would like to paired the forward and reverse before I truncate sequences. I try to do qiime 2 dada2 denoised-paired --help. But it did not show a command to execute this. Can you help me on this please ?

Thank you.

[cherman2 (Chloe Herman)]

Hello @nbezia01,
I don't believe that dada2 does what you are wanting.
If you want to join your sequences before quality control. I would recommend checking out our Alternative methods of read-joining. This will have you join your reads and then run deblur for quality control. Does that sound like what you are looking for?

If you want to use dada2 then you will have to trim prior to joining.
Hope that helps!
Chloe