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Old 07-30-2016, 02:18 PM   #3
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

Very few mappers have support for circular genomes (e.g. CLC mapper), and worse, the SAM/BAM format does not handle this well. As suggested by Tristan, mapping to a doubled linear reference can be a useful alternative (but brings with it a lot of complications).

If you are mainly interested in mapping to the origin region of a circular chromosome, it would be simpler to make a linear chromosome split elsewhere in the circle, and map to that.
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