Dada2 denoise-paired: how much to trunc and trim?

User Support
1

Hi all,

I am denoising samples using:
qiime dada2 denoise-paired
–i-demultiplexed-seqs
–p-trunc-len-f
–p-trunc-len-r
–p-trim-left-f
–p-trim-left-r
–p-chimera-method consensus
–o-table
–o-representative-sequences
/scratch/tcarrie1/Lv_DevPlas/analysis_bacteria/qiime2_SILVA99/Lv_DiffFeeding_DenoiseStats.qza
–verbose

What are suggested values for?:
–p-trunc-len-f
–p-trunc-len-r
–p-trim-left-f
–p-trim-left-r

Regards,
Tyler

PS - Hey, Evan! Hope all is well! Thanks for all your work with our q2 issues! You rock! :slight_smile:

1 Like
2

Oh man, welcome to the forum Tyler!

Those values really depend on your quality scores, you're looking for a natural break in the data on the trunc-len, and for the trim-left, that's to remove your primers, etc.

The moving pictures tutorial talks about this a bit.

3

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