mothur

Screen.seqs after alignment

Hi there!!!
after alignment I’ve got this result:

Using 8 processors.


		Start	End	NBases	Ambigs	Polymer	NumSeqs
Minimum:	0	0	0	0	1	1
2.5%-tile:	2	17017	403	0	4	10266
25%-tile:	2	17018	404	0	4	102657
Median: 	2	17018	413	0	5	205314
75%-tile:	2	17018	424	0	5	307971
97.5%-tile:	4	17018	429	4	7	400362
Maximum:	17063	17065	459	104	220	410627
Mean:	94	16931	410	0	4
# of unique seqs:	218440
total # of seqs:	410627

It took 34 secs to summarize 410627 sequences.

Is the following screen.seqs command enough to discard ‘‘bad’’ sequences? Or, should I add maxlength and/or minlength option with this?

screen.seqs(fasta=current, count=current, maxambig=0, maxhomop=8, start=2, end=17018)

Thanks and Regards,
DC7

that should be fine. as i think i said before, you really should run this on the reference sequences that have been trimmed for your region after removing the primers to make sure you have the right range of min/max length.