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

[Negin]

Yes, I used Safari instead of Google chrome and was able to see it for a few seconds. Unfortunately, the seven-numbers file only shows values above 2% and below 98%. The actual values have a min of 52 and maximum of 1871 so there are erroneous reads there. I can either remove those but then I really don’t know what the expected range is or to find the expected range. The original paper that introduced eubf-eubr mentions amplicon size of 466 bps but does not specify a range.

Also, this length, does it include the primer as well since we are removing the primers in dada2.

[Nicholas_Bokulich]

@Negin

The actual values have a min of 52 and maximum of 1871 so there are erroneous reads there.

Okay yes that is too wide of a range. You should set some lower and upper limits.

@Negin

The original paper that introduced eubf-eubr mentions amplicon size of 466 bps but does not specify a range.

100 nt to either side is probably wide enough.

@Negin

Also, this length, does it include the primer as well since we are removing the primers in dada2.

If you mean for extract-reads, no it is length without primers.