Pcr.seqs with Silva 138 start/end

Commands in mothur
1

Hello,

When I run pcr.seqs with my oligos file and subsequent summary.seqs I get the following summary:

Start End NBases Ambigs Polymer NumSeqs
Minimum: 1115 22545 45 0 3 1
2.5%-tile: 13862 23444 252 0 3 2897
25%-tile: 13862 23444 253 0 4 28970
Median: 13862 23444 253 0 4 57940
75%-tile: 13862 23444 253 0 5 86909
97.5%-tile: 13862 23444 255 0 6 112982
Maximum: 13875 26105 714 5 16 115878
Mean: 13861 23444 253 0 4

Typically, when I have run this in the past I get the same start and end from minimum to maximum. This time around I get different minimum values and maximum values. What do you advise that I use for my start/end points? I am concerned if I use start =13862 and end = 23444 I will be missing taxa that may be important or getting incorrect alignments.

Thanks in advance and hope your quarantine is going well!

2

You should use start=13862 and end=23444. You’re unlikely to lose many sequences doing this. If you look at the MiSeq SOP output from summary.seqs after running align.seqs, you’ll see that we got somewhat similar results.

Pat

1 Like
3

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.