Question: Ungapped Alignment In Bwa
1
gravatar for Higherdefender
9.7 years ago by
India
Higherdefender130 wrote:

Hi,

I am new to the field of bioinformatics. Currently, I am playing with bwa sequence alignment tool. As I read through the manual, I couldn't understand how to do un-gapped alignments in "bwa"(short read one)(default option is gapped). This is a very rookie question and of no use, but I need to do it for comparison purposes and I just can't figure it out. Please help.

Thanks.

P.S. Is it done by setting option -M to 0?

next-gen bwa sequencing • 3.0k views
ADD COMMENTlink written 9.7 years ago by Higherdefender130
4
gravatar for Docroberson
9.7 years ago by
Docroberson300
the lab
Docroberson300 wrote:

I haven't tried to do an ungapped alignment with BWA, but I would think setting "-o 0" would disable gapping by setting the maximum number of gap openings to 0.

ADD COMMENTlink written 9.7 years ago by Docroberson300
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