Min and Max primer length

[Hanna1 (Hannah M O'Connor)]

Trying to train the classifier on a reference database with our specifics- How do you work out primer min and max length? Using primer F926 and R1392 generating a 500BP product.

qiime feature-classifier extract-reads **
–i-sequences 99_otus.qza **
–p-f-primer TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAAACTYAAAKGAATTGRCGG **
–p-r-primer GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGACGGGCGGTGWGTR **
–p-trunc-len 267 **
–p-min-length 200 **
–p-max-length 500 **
–o-reads ref-seqs.qza

[lizgehret]

Hi Hannah,

Thanks for reaching out, happy to provide some guidance here!

The --p-min-length and --p-max-length parameters are actually in reference to your amplicon lengths (rather than the primer lengths). These parameters are defined as follows:

--p-min-length: Minimum amplicon length. Shorter amplicons are discarded. Applied after trimming and truncation, so be aware that trimming may impact sequence retention. Set to zero to disable min length filtering.

--p-max-length: Maximum amplicon length. Longer amplicons are discarded. Applied after trimming and truncation, so be aware that trimming may impact sequence retention. Set to zero (default) to disable max length filtering.

More details on all of the inputs and parameters for extract-reads can be found by running the following command:

qiime feature-classifier extract-reads --help

Hope this helps; don’t hesitate to reach back out if you have any further questions!