Training feature classifier: values for --p-trunc-len; --p-min-length; and --p-max-length

[Nicholas_Bokulich]

@Negin

I ran these codes and there isn’t a seven_number_summary in the data folder. I checked there physically in addition to running the code.

Sounds like you running an older release of QIIME 2. This length summary was added a couple releases ago, I believe.

@Negin

found this link that seems to show between 100-500 for v3v4 which should work for me although my primer is a bit longer

As long as the primers are hitting the same site, you can go off that info

Another good place to get info like this is the forum! Here is a recent topic describing expected length for V3V4, though the length range is not stated, only (presumably) the mean:

DADA2, truncation parameters question

Hello, I have a question about truncation parameters for a 2x300 bp paired end run using the V3-V4 region. These results are with the primers removed (341F and 805R). Here is the visualization of demux.qzv after trimming primers using cutadapt. [Picture1] My first data point is with reads that have been truncated at --p-trunc-len-f 281 and -p--trunc-len-r 202. Theoretically, these limits should be fine given that the expected amplicon size is around ~460 bp. This should leave enough for the ~…

Based on these findings, 300-600 is probably a fine, permissive range for you to use (though in practice the variance is probably much less, since most 16S regions don't have that much length variation)