How to decide maxlength when i want to analyze data from different experiments?

Commands in mothur
1

How to decide maxlength when i want to analyze data from different experiments?

Start   End     NBases  Ambigs  Polymer NumSeqs
Minimum:        1       35      35      0       2       1
2.5%-tile:      1       304     304     0       4       49928
25%-tile:       1       333     333     0       4       499280
Median:         1       400     400     0       4       998560
75%-tile:       1       445     445     0       5       1497840
97.5%-tile:     1       470     470     9       6       1947192
Maximum:        1       602     602     256     300     1997119
Mean:   1       377     377     0       4
# of unique seqs:       1997119
total # of seqs:        1997119

this is my summary.seqs result

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Hi - it looks like you used 2x300 nt chemistry. You’ll need to generate a custom version of the silva reference alignment for your region to see which values of minlength/maxlength make the most sense. Clearly 602 is not good, but I suspect 35 isn’t good either.

You’ll also likely want to consult this blog post on using chemistries other than the 2x250 chemistry

Pat

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