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Old 07-28-2016, 07:44 AM   #1
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Location: DC

Join Date: Jan 2015
Posts: 4
Default How Do Mappers Handle Chromosome Ends?

I am trying to figure out how BW-based mappers like BWA and Bowtie handle reads that map at the end of the reference and extend off the end. One example would be reads from the origin of a circular chromosome, where part maps to the beginning of the sequence used to build the index, and part of it maps to the very end. How are such reads scored? Is each extending base considered a mismatch, gap extension, or something else?

Thanks in advance!

NOTE:Also posted on Biostars
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