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Old 05-29-2013, 04:25 AM   #1
Location: UK

Join Date: May 2012
Posts: 12
Default NUCmer dotplot orientation

Dear Experts,
I did some dotplots (using NUCmer default settings) for comparing chromosome-scale pseudomolecules from two different versions of the same species. Two of the result plots are attached.

Normally I would expect dotplots to start from '0, 0' x and y axes positions (e.g. figure A) as sequence order in both versions is same. However, for some chromosomes NUCmer is generating dotplots starting from end positions (figure B) which makes it look as if one of the chromosomes is inverted.

I straight interpretation from this would be that one of the chromosomes is inverted. However, after talking to some people it appears that NUCmer/Mummer may pick one direction arbitrarily, is it true? Can MUMmer give this type of output without the two input files necessarily being in the inverse orientation??

I would highly appreciate any feedback on this issue.

Attached Files
File Type: pdf Nucmer_Dotplots_query.pdf (40.9 KB, 24 views)
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