MOTHUR:16s analysis: maximum ambiguity

0

Entering edit mode

3.9 years ago

dpc ▴ 240

Hi friends!!! I am using mothur for analysing 16s rRNA gene sequence analysis. Can you please tell me how much ambiguity (maxambig=?) should I use in my protocol?

16s mothur ambiguity protocol • 1.0k views

ADD COMMENT • link 3.9 years ago by dpc ▴ 240

0

Entering edit mode

maxambig = x

x = maximum number of ambiguous bases in a given read?

ADD REPLY • link 3.9 years ago by 5heikki 11k

0

Entering edit mode

Sorry, I can't understand. Can you please elaborate a little?

ADD REPLY • link 3.9 years ago by dpc ▴ 240

0

Entering edit mode

Bacterial genomes typically have multiple copies of the 16S rRNA gene, which are not necessarily identical. When you sequence DNA, the basecaller algorithm may e.g. see a position where A and G are as common and call the position as R, which is IUPAC code for A or G. I presume in mothur maxambig controls how many such bases you want to allow in a sequence before it's discarded

ADD REPLY • link 3.9 years ago by 5heikki 11k

0

Entering edit mode

yes.... actually that is my question. How many ambiguous base should I keep in my sequence at most for doing taxonomic analysis in MOTHUR,

ADD REPLY • link 3.9 years ago by dpc ▴ 240

0

Entering edit mode

How many sequences are discarded if you allow 0, 1, 2, etc.?

ADD REPLY • link 3.9 years ago by 5heikki 11k

0

Entering edit mode

Hi...I have to check and let you know. Can you please answer this query also?

ADD REPLY • link 3.9 years ago by dpc ▴ 240

Login before adding your answer.