Hi- I have performed alignment without any prior screening. After alignment (withalign.seqs
) I am getting such sequence distribution:
Using 16 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 11550 231 0 3 1
2.5%-tile: 1968 11550 252 0 3 261901
25%-tile: 1968 11552 253 0 4 2619004
Median: 1968 11552 254 0 4 5238007
75%-tile: 1968 11552 254 5 4 7857010
97.5%-tile: 1968 11552 254 9 6 10214113
Maximum: 1968 13424 284 25 126 10476013
Mean: 1967 11553 253 2 3
# of unique seqs: 3276106
total # of seqs: 10476013
Now I am screening sequences with following command with different maxambig
values:
mothur > screen.seqs(fasta=stability.trim.contigs.unique.align, count=stability.trim.contigs.count_table, start=1968, end=11550, maxambig=0)
maxambig=0
removes 45% sequences
maxambig=1
removes 41% sequences
maxambig=2
removes 36% sequences
maxambig=3
removes 34% sequences
Can you please suggest me what should be my ideal maxambig value in this case?
Thanks,
DC7