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maxambig = x
x = maximum number of ambiguous bases in a given read?
Sorry, I can't understand. Can you please elaborate a little?
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
yes.... actually that is my question. How many ambiguous base should I keep in my sequence at most for doing taxonomic analysis in MOTHUR,
How many sequences are discarded if you allow 0, 1, 2, etc.?
Hi...I have to check and let you know. Can you please answer this query also?