Question: Bwa Gapped Alignment
0
gravatar for Bioscientist
8.2 years ago by
Bioscientist1.7k
Bioscientist1.7k wrote:

bwa aln has the option "-o INT Maximum number of gap opens [1] " Does this mean by default maximum only 1 gap is allowed?

However, I ran BWA by default and I can see lots of my alignment includes say 5bp, 10bp gaps. How to explain this?

thx

bwa • 2.3k views
ADD COMMENTlink written 8.2 years ago by Bioscientist1.7k
2
gravatar for Manu Prestat
8.2 years ago by
Manu Prestat4.0k
Lyon, France
Manu Prestat4.0k wrote:

I guess that you can have a single gap of length 10pb. This is still one gap.

ADD COMMENTlink written 8.2 years ago by Manu Prestat4.0k

ok, i see..One gap can contain many bases....actually my gap can include 20bp as far as I see.

ADD REPLYlink written 8.2 years ago by Bioscientist1.7k
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