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


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.


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
gravatar for Docroberson
9.7 years ago by
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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2289 users visited in the last hour