MATLAB Answers


Method to include insertions in compact alignment from BioMap object?

Asked by Turner
on 25 May 2013

Hi all,

I'm working with a BioMap object containing 50bp sequencing reads from a BAM file. My goal is to retrieve a full genome sequence from the BioMap. So far, I know how to use getCompactAlignment to get a memory-friendly version of an alignment that can be converted into a consensus sequence. I've mastered how to handle deletions, but getCompactAlignment does not account for insertions, and actually removes them from the alignment. Is there another method to generate a compact alignment or direct consensus sequence from a BioMap that includes insertions?


0 Answers

Discover what MATLAB® can do for your career.

Opportunities for recent engineering grads.

Apply today