Question: MOTHUR:16s analysis: maximum ambiguity
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gravatar for DC7
5 weeks ago by
DC720
India
DC720 wrote:

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?

protocol 16s mothur ambiguity • 107 views
ADD COMMENTlink written 5 weeks ago by DC720

maxambig = x

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

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by 5heikki8.8k

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

ADD REPLYlink written 5 weeks ago by DC720

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 REPLYlink modified 5 weeks ago • written 5 weeks ago by 5heikki8.8k

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 REPLYlink written 4 weeks ago by DC720

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

ADD REPLYlink written 4 weeks ago by 5heikki8.8k

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

ADD REPLYlink written 4 weeks ago by DC720
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