Filtering sequence based on size and/or quality

[David_Pearton]

Hello,

New user here so I apologise if this has been answered already.

I’m running Qiime2 2019.4 on virtualbox 6.0.
I have 2 X 300 paired end miseq data that contains a lot of primer dimers and truncated reads. It there any way of removing these “rubbish” sequenced before denoising with dada2?

The truncated sequences make it look like the first 32 bases are very poor quality overall but I think that the full length sequences are actually fine so I don’t want to trim away useful sequence by using the trim command too aggressively.

Thank you.

[colinbrislawn (Colin J Brislawn)]

Hello David,

Welcome to the Qiime forums!

You are asking all the right questions, and I say that because these are exactly the topics covered in the tutorials about dada2, especially this part of the Atacama Soils tutorial

@David_Pearton

The truncated sequences make it look like the first 32 bases are very poor quality overall but I think that the full length sequences are actually fine so I don’t want to trim away useful sequence by using the trim command too aggressively.

Sounds like you need --p-trim-left-f 32!
See what else you might want to try out from that tutorial.

Colin